TINKER
Software Tools for Molecular Design
Version 8.1
February 2017
Copyright © 1990-2017 by Jay William Ponder
All Rights Reserved
Copyright © 1990-2017 by Jay William Ponder
All Rights Reserved
User's Guide Cover Illustration by Jay Nelson
Courtesy of Prof. R. T. Paine, Univ. of New Mexico
TINKER IS PROVIDED "AS IS" AND WITHOUT ANY WARRANTY
EXPRESS OR IMPLIED. THE USER ASSUMES ALL RISKS OF
USING THIS SOFTWARE. THERE IS NO CLAIM OF THE
MERCHANTABILITY OR FITNESS FOR A PARTICULAR
PURPOSE.
YOU MAY MAKE COPIES OF TINKER FOR YOUR OWN USE,
AND MODIFY THOSE COPIES. YOU MAY NOT DISTRIBUTE ANY
MODIFIED SOURCE CODE OR DOCUMENTATION TO USERS AT
ANY SITE OTHER THAN YOUR OWN. PLEASE SIGN AND
RETURN THE TINKER LICENSE AGREEMENT IF YOU MAKE
USE OF THIS SOFTWARE.
V8.1.1 2/17
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TINKER User's Guide
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TINKER
Software Tools for Molecular Design
Version 8.1 February 2017
Table of Contents
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15.
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Page
Introduction to the Software
Installation on your Computer
Types of Input & Output Files
Potential Energy Programs
Additional Utility Programs & Scripts
Special Features & Methods
Use of the Keyword Control File
Force Field Parameter Sets
Descriptions of Source Routines
Descriptions of Global Variables
Index of Function & Subroutine Calls
Test Cases & Examples
Benchmark Results
Collaborators & Acknowledgments
References & Suggested Reading
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1.
IntroductiontotheSoftware
WhatistheTINKERSoftware?
WelcometotheTINKERmolecularmodelingpackage!TINKERisdesignedtobeaneasilyusedand
flexible system of programs and routines for molecular mechanics and dynamics as well as other
energy-basedandstructuralmanipulationcalculations.Itisintendedtobemodularenoughtoenable
development of new computational methods and efficient enough to meet most production
calculationneeds.Ratherthanincorporatingallthefunctionalityinonemonolithicprogram,TINKER
providesasetofrelativelysmallprogramsthatinteroperatetoperformcomplexcomputations.New
programscanbeeasilyaddedbymodelerswithonlylimitedprogrammingexperience.
FeaturesandCapabilities
Theseriesofmajorprogramsincludedinthedistributionsystemperformthefollowingcoretasks:
(1)
(2)
(3)
(4)
(5)
(6)
(7)
(8)
(9)
(10)
(11)
(12)
(13)
buildingproteinandnucleicacidmodelsfromsequence
energyminimizationandstructuraloptimization
analysisofenergydistributionwithinastructure
moleculardynamicsandstochasticdynamics
simulatedannealingwithachoiceofcoolingschedules
normalmodesandvibrationalfrequencies
conformationalsearchandglobaloptimization
transitionstatelocationandconformationalpathways
fittingofenergyparameterstocrystaldata
distancegeometrywithpairwisemetrization
molecularvolumesandsurfaceareas
freeenergychangesforstructuralmutations
advancedalgorithmsbasedonpotentialsmoothing
Many of the various energy minimization and molecular dynamics computations can be performed
onfullorpartialstructures,overCartesian,internalorrigidbodycoordinates,andincludingavariety
ofboundaryconditionsandcrystalcelltypes.Otherprogramsareavailabletogeneratetimingdata
andallowcheckingofpotentialfunctionderivativesforcodingerrors.Specialfeaturesareavailable
tofacilitateinputandoutputofproteinandnucleicacidstructures.However,thebasiccoreroutines
havenoknowledgeofbiopolymerstructureandcanbeusedforgeneralmolecularsystems.
Due to its emphasis on ease of modification, TINKER differs from many other currently available
molecularmodelingpackagesinthattheuserisexpectedtobewillingtowritesimple``front-end''
programsandmakesomealterationsatthesourcecodelevel.Themainprogramsprovidedshould
be considered as templates for the users to change according to their wishes. All subroutines are
internallydocumentedandstructuredprogrammingpracticesareadheredtothroughout.Theresult,
itishoped,willbeacalculationalsystemwhichcanbetailoredtolocalneedsanddesires.
The core TINKER system consists of nearly 135,000 lines of source written entirely in a portable
Fortran77 superset. Use is made of only some very common extensions that aid in writing highly
structuredcode.Thecurrentversionofthepackagehasbeenportedtoawiderangeofcomputers
withnoorextremelyminimalchanges.Testedsystemsinclude:RedHatLinux,MicrosoftWindows
9X/NT/2000/XP, Apple OS9 and OSX, HP/Compaq/DEC Alphas under Tru64 Unix and OpenVMS,
Hewlett-Packard,IBM,SiliconGraphicsandSunworkstationsundereachvendor'sUnix.Atpresent,
our new code is written on various Linux platforms, and occasionally tested for compatibility on
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variousoftheothermachineandOScombinationslistedabove.Atpresent,weareintheprocessof
converting our primary development efforts from Fortran77 to a more modern Fortran dialect. A
machine-translated C version of TINKER is currently available, and a hand-translated optimized C
version of a previous TINKER release is available for inspection. Conversion to C or C++ is under
consideration,butnotbeingactivelypursuedatthistime.
ThebasicdesignoftheenergyfunctionengineusedbytheTINKERsystemallowsusageofseveral
differentparametersets.AtpresentwearedistributingparametersthatimplementAMBERff94and
ff96,CHARMM19and27,MM2,MM3,OPLS-UA,OPLS-AA,LiamDang'spolarizablepotentials,andour
ownAMOEBA(AtomicMultipoleOptimizedEnergeticsforBiomolecularApplications)parameters.In
most cases, the source code separates the geometric manipulations needed for energy derivatives
fromtheactualformoftheenergyfunctionitself.Severalotherliteratureparametersetsarebeing
considered for possible future development (ENCAD, MMFF-94, MM4, UFF, etc.), and many of the
alternative potential function forms reported in the literature can be implemented directly or after
minorcodechanges.
Much of the software in the TINKER package has been heavily used and well tested, but some
modules are still in a fairly early stage of development. Further work on the TINKER system is
planned in three main areas: (1) extension and improvement of the potential energy parameters
including additional parameterization and testing of our polarizable multipole AMOEBA force field,
(2) coding of new computational algorithms including additional methods for free energy
determination,torsionalMonteCarloandmoleculardynamicssampling,advancedmethodsforlong
rangeinteractions,bettertransitionstatelocation,andfurtherapplicationofthepotentialsmoothing
paradigm, and (3) further development of Force Field Explorer, a Java-based GUI front-end to the
TINKERprogramsthatprovidesforcalculationsetup,launchandcontrolaswellasbasicmolecular
visualization.
ContactInformation
Questions and comments regarding the TINKER package, including suggestions for improvements
andchangesshouldbemadetotheauthor:
ProfessorJayWilliamPonder
DepartmentofChemistry,Box1134
WashingtonUniversityinSaintLouis
OneBrookingsHall
SaintLouis,MO 63130 U.S.A.
office:
phone:
fax:
email:
LoudermanHall,Room453
(314)935-4275
(314)935-4481
[email protected]
In addition, an Internet web site containing an online version of this User's Guide, the most recent
distribution version of the full TINKER package and other useful information can be found at
http://dasher.wustl.edu/tinker, the Home Page for the TINKER Molecular Modeling
Package.
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2.
InstallationonyourComputer
How to Obtain a Copy of TINKER
The TINKER package is distributed on the Internet via either the web site or the anonymous ftp
accountondasher.wustl.eduwithanIPnumberof128.252.208.48.Thisnodeisawebandfile
server located in the Ponder lab at Washington University School of Medicine. The package is
available via the web and standard browsers from the TINKER home page at
http://dasher.wustl.edu/tinker/. Alternatively TINKER can be downloaded by logging
into dasher.wustl.edu via anonymous ftp (Username: anonymous, Password: "your email
address")anddownloadingthesoftwarefromthe/pub/tinkersubdirectory.ThecompleteTINKER
distributionsaswellasindividualfilescanbedownloadedfromthissite.
TheeasiestwaytogetTINKERrunningonyourmachineistousetheself-extractinginstallationkit
for either Linux, Windows, or Macintosh OS X 10.3. The installer will guide you through complete
setup of TINKER and the Force Field Explorer (FFE) GUI, and perform all required configuration
chores. The installer kits for the three supported systems are tinker4.2-linux.sh,
tinker4.2-windows.exe and tinker4.2-macosx.sit. The Linux and Windows kits each
contain a private copy of a Java and Java3D run-time environment for use with the package. The
Macintosh version requires an OS X 10.3 (Panther) system for installation. The native Java
implementation is used on Macs, and the Java3D package must be downloaded from Apple and
installedpriortousingTINKERwithForceFieldExplorer.
PrebuiltTINKERExecutables
TheTINKERpackageisalsoavailableascompressedUnixtararchives,Windowszipfiles,andasa
complete set of uncompressed source and data files. Binaries are provided for machines running
Windows 9X/ME/NT/2000/XP, Linux, and Apple Mac OS X. All of these executables are present in
standard compressed formats as individual programs or as complete sets of executables. It is
expected that other Unix users and PC users who need specially customized versions, will build
binaries for their specific system. Sites with access to the Unix tar, compress and uncompress
commands should simply obtain the archive file tinker.tar.Z. Alternatively, tinker.tar.gz
and tinker.zip containing identical distributions compressed to GNU gzip and Windows ZIP
formatarealsoprovided.Ifyouchoosetodownloadindividualfiles,youwillneedataminimumthe
contents of the /doc, /source and /params subdirectories. Also required are the compile/build
scripts from the subdirectory named for your machine type. Other areas contain test cases and
examples,benchmarkresults,machine-translatedCcode,andtheForceFieldExplorerJavaGUIfor
TINKER. The entire TINKER package, after building the executables, will require from about 40 to
over 150 megabytes of disk space depending on the components installed and the use of shared
librariesintheexecutables.
Building your Own Executables
The compilation and building of the TINKER executables should be easy for most of the common
workstationandPCclasscomputers.Weprovideinthe/makeareaaUnix-styleMakefilethatwith
somemodificationcanbeusedtobuildTINKERonmostUnixmachines.Asasimpleralternativeto
Makefiles for the Unix versions, we also provide machine-specific directories with three separate
shellscriptstocompilethesource,buildanobjectlibrary,andlinkbinaryexecutables.Threesimilar
command files are provided for Windows, Macintosh and Open VMS systems. Compilation on Unix
workstationsshouldusethevendorsuppliedFortrancompiler,ifavailable.ThepublicdomainGNU
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g77 Fortran compiler available from http://gcc.gnu.org/ is also capable of building TINKER
onLinuxandotherUnix-basedmachines.TheLinuxexecutablesweprovidearebuiltwiththeIntel
FortranforLinux8.0compiler.ThePortlandGroup(PGI)andAbsoftProFortrancompilershavealso
been tested under Linux, both of which generate executables roughly comparable in speed to the
Intelcompiler.OnLinux,theg77executablestendtoexhibitdegradedperformancecomparedwith
executablesfromcommercialcompilers.Somebenchmarkresultsareprovidedinalatersectionof
thisUser'sGuideFortheMacintoshwedistributeexecutablesbuiltunderAppleOSX10.3withthe
GNUg77compiler.TINKERalsobuildsontheMacintoshusingtheAbsoftProFortrancompiler.For
PCsrunningWindows9X/NT/2000/XP,thedistributedTINKERexecutablesarebuiltundertheIntel
FortranforWindows8.0compiler.AlternativeWindowscompilerssuchasCompaqVisualFortran,
Lahey/FujitsuandThePortlandGroupcompilers,andGNUg77underCygwinhavebeentestedand
showntobuildTINKERcorrectly.PleaseseetheREADMEfilesineachofthemachine-specificareas
forfurtherinformation.
The first step in building TINKER using the script files is to run the appropriate
compile.make script for your operating system and compiler version. Next you must use a
library.makescripttocreateanarchiveofobjectcodemodules.Finally,runalink.makescript
toproducethecompletesetofTINKERexecutables.Theexecutablescanberenamedandmovedto
whereveryoulikebyeditingandrunningthe``rename''script.Thesestepswillproduceexecutables
thatcanrunfromthecommandline,butwithoutthecapabilitytointeractwiththeFFEGUI.Building
FFE-enabledTINKERexecutablesinvolvesreplacingthesockets.fsourcefilewithsockets.c,and
included the object from the C code in the TINKER object library. Then executables must be linked
against Java libraries in addition to the usual resources. Sample compgui.make and
linkgui.makescriptsareprovidedforsystemscapableofbuildingGUI-enabledexecutables.
Regardless of your target machine, only a few small pieces of code can possibly require
attentionpriortobuilding.Thefirsttwoarethesystemdependenttimeanddateroutinesfoundin
clock.fandcalendar.frespectively.Nextistheopenend.froutinethatfacilitatesappending
datatotheendofanexistingdiskfile.Pleaseuncommentthesectionsoftheseroutinesneededfor
your computer type. Version of these system dependent routines suitable for each system are also
providedinthedirectoryforeachmachine/OStype.Thefinalsetofpossiblesourcealterationsareto
the master array dimensions found in the include file sizes.i. The most basic limit is on the
number of atoms allowed, ``maxatm''. This parameter can be set to 10000 or more on most
workstations. Personal computers with minimal memory may need a lower limit, perhaps 1000
atoms,dependingonavailablememory,swapspaceandotherresources.Adescriptionoftheother
parametervaluesiscontainedintheheaderofthefile.Notethatinordertokeepthecodecompletely
transparent, TINKER does not implement any sort of dynamic memory allocation or heap data
structure. This requires that sizes.i dimensioning values be set at least as large as the biggest
problem you intend to run. Obviously, you should not set the array sizes to unnecessarily large
values, since this can tax your compute resources and may result in performance degradation or
overtfailureoftheexecutables.
DocumentationandOtherInformation
The documentation for the TINKER programs, including the guide you are currently reading, is
locatedinthe/pub/tinker/docsubdirectory.ThedocumentationwaspreparedusingtheApplixware
WordsandGraphicsprograms.Portableversionsofthedocumentationareprovidedasasciitextin
.txt files and in Adobe Acrobat .pdf file formats. Please read and return by mail the TINKER
license. In particular, we note that TINKER is not ``Open Source'' as users are prohibited from
redistribution of original or modified TINKER source code or binaries to other parties. While our
intentistodistributetheTINKERcodetoanyonewhowantsit,thePonderLabwouldliketoremain
thesoledistributionsiteandkeeptrackofresearchersusingthepackage.Thereturnedlicenseforms
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also help us justify further development of TINKER. When new modules and capabilities become
available, and when the almost inevitable bugs are uncovered, we will attempt to notify those who
havereturnedalicenseform.Finally,weremindyouthatthissoftwareiscopyrighted,andaskthatit
notberedistributedinanyform.
WheretoDirectQuestions
Specific questions about the building or use of the TINKER package should be directed to
[email protected]. TINKER related questions or comments of more general interest
canbesenttotheComputationalChemistryList(http://www.ccl.net/)runbyJanLabanowski
attheUniversityofNotreDame.TheTINKERdevelopersmonitorthislistandwillrespondtothelist
ortheindividualposterasappropriate.
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3.
TypesofInput&OutputFiles
ThissectiondescribesthebasicfiletypesusedbytheTINKERpackage.Let'ssayyouwishtoperform
acalculationonaparticularsmallorganicmolecule.Assumethatthefilenamechosenforourinput
andoutputfilesissample.ThenalloftheTINKERfileswillresideonthecomputerunderthename
sample.xxxwhere.xxxisanyoftheseveralextensiontypestobedescribedbelow.
SAMPLE.XYZ
The.xyzfileisthebasicTINKERCartesiancoordinatesfiletype.Itcontainsatitlelinefollowedby
one line for each atom in the structure. Each line contains: the sequential number within the
structure,anatomicsymbolorname,X-,Y-,andZ-coordinates,theforcefieldatomtypenumberof
the atom, and a list of the atoms connected to the current atom. Except for programs whose basic
operation is in torsional space, all TINKER calculations are done from some version of the .xyz
format.
SAMPLE.INT
The.intfilecontainsaninternalcoordinatesrepresentationofthemolecularstructure.Itconsists
ofatitlelinefollowedbyonelineforeachatominthestructure.Eachlinecontains:thesequential
number within the structure, an atomic symbol or name, the force field atom type number of the
atom,andinternalcoordinatesintheusualZ-matrixformat.Foreachatomtheinternalcoordinates
consist of a distance to some previously defined atom, and either two bond angles or a bond angle
and a dihedral angle to previous atoms. The length, angle and dihedral definitions do not have to
represent real bonded interactions. Following the last atom definition are two optional blank line
separatedsetsofatomnumberpairs.Thefirstlistcontainspairsofatomsthatarecovalentlybonded,
butwhosebondlengthwasnotusedaspartoftheatomdefinitions.Thesepairsaretypicallyusedto
closeringstructures.Thesecondlistcontains``bonds''thataretobebroken,i.e.,pairsofatomsthat
arenotcovalentlybonded,butwhichwereusedtodefineadistanceintheatomdefinitions.
SAMPLE.KEY
Thekeywordparameterfilealwayshastheextension.keyandisoptionallypresentduringTINKER
calculations.Itcontainsvaluesforanyofawidevarietyofswitchesandparametersthatareusedto
changethecourseofthecomputationfromthedefault.Thedetailedcontentsofthisfileisexplained
in a latter section of this User's Guide. If a molecular system specific keyfile, in this case
sample.key,isnotpresent,thetheTINKERprogramwilllookinthesamedirectoryforageneric
filenamedtinker.key.
SAMPLE.DYN
The.dynfilecontainsvaluesneededtorestartamolecularorstochasticdynamicscomputation.It
storesthecurrentposition,currentvelocityandcurrentandpreviousaccelerationsforeachatom,as
well as the size and shape of any periodic box or crystal unit cell. This information can be used to
startanewdynamicsrunfromthefinalstateofapreviousrun.Uponstartup,thedynamicsprograms
alwayscheckforthepresenceofa.dynfileandmakeuseofitwheneverpossible.The.dynfileis
updatedconcurrentwiththesavingofanewdynamicstrajectorysnapshot.
SAMPLE.END
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The .end file type provides a mechanism to gracefully stop a running TINKER calculation. At
appropriate checkpoints during a calculation, TINKER will test for the presence of a sample.end
file, and if found will terminate the calculation after updating the output. The .end file can be
createdatanytimeduringacomputation,andwillbedetectedwhenthenextcheckpointisreached.
Thefilemaybeofzerosize,anditscontentsareunimportant.InthecurrentversionofTINKER,the
.endmechanismisonlyavailablewithindynamics-basedprograms.
SAMPLE.001,SAMPLE.002,....
Several types of computations produce files containing a three or more digit extension (.001 as
shown;or.002,.137,.5678,etc.).Thesearereferredtoascyclefiles,andareusedtostorevarious
typesofoutputstructures.Thecyclefilesfromagivencomputationareidenticalininternalstructure
toeitherthe.xyzor.intfilesdescribedabove.Forexample,thevibrationalanalysisprogramcan
savethetenthnormalmodeinsample.010.Amoleculardynamics-basedprogrammightsaveits
tenth0.1picosecondframe(oranenergyminimizeritstenthpartiallyminimizedintermediate)ina
fileofthesamename.
SAMPLE.LOG
TheForceFieldExplorerinterfacetoTINKERsavesresultsofallcalculationslaunchedfromtheGUI
to a log file with the .log suffix. Any output that would normally be directed to the screen after
startingaprogramfromthecommandlineisappendedtothislogfilebyForceFieldExplorer.
SAMPLE.ARC
A TINKER archive file is simply a series of .xyz Cartesian coordinate files appended together one
after another. This file can be used to condense the results from intermediate stages of an
optimization,framesfromamoleculardynamicstrajectory,orsetofnormalmodevibrationsintoa
singlefileforstorage.TINKERarchivefilescanbedisplayedas``movies''bytheForceFieldExplorer
modelingprogram.
SAMPLE.PDB
This file type contains coordinate information in the PDB format developed by the Brookhaven
ProteinDataBankfordepositionofmodelstructuresbasedonmacromolecularX-raydiffractionand
NMR data. Although TINKER itself does not use .pdb files directly for input/output, auxiliary
programs are provided with the system for interconverting .pdb files with the .xyz format
describedabove.
SAMPLE.SEQ
Thisfiletypecontainstheprimarysequenceofabiopolymerinthestandardone-lettercodewith50
residues per line. The .seq file for a biopolymer is generated automatically when a PDB file is
converted to TINKER .xyz format or when using the PROTEIN or NUCLEIC programs to build a
structure from sequence It is required for the reverse conversion of a TINKER file back to PDB
format..
SAMPLE.FRAC
The fractional coordinates corresponding to the asymmetric unitof a crystal unit cell are stored in
the.fracfile.Theinternalformatofthisfileisidenticaltothe.xyzfile;exceptthatthecoordinates
arefractionalinsteadofinAngstromunits.
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SAMPLE.XMOL
The ARCHIVE program has the option of converting a series of .xyz cycle files into an XMakemol
XYZfile.ThesefilescanbedisplayedasamovieusingtheXMakemoldisplayprogram.Notethatthe
.xmolfileformatdoesnotcontainTINKERatomtypeinformation,soitisnotpossibletoconvertan
.xmolfilebackintoaTINKER.xyzfile.
SAMPLE.CAR
The ARCHIVE program has the option of converting a series of .xyz cycle files into an Accelerys
InsightII coordinate archive file. These files can be displayed as a movie using the InsightII display
program.Notethatthe.carfileformatdoesnotcontainTINKERatomtypeinformation,soitisnot
possibletoconverta.carfilebackintoaTINKER.XYZfile.
PARAMETERFILES
The potential energy parameter files distributed with the TINKER package all end in the extension
.prm, although this is not required by the programs themselves. Each of these files contains a
definitionofthepotentialenergyfunctionalformsforthatforcefieldaswellasvaluesforindividual
energy parameters. For example, the mm3pro.prm file contains the energy parameters and
definitionsneededforaprotein-specificversionoftheMM3forcefield.
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4.
PotentialEnergyPrograms
This section of the manual contains a brief description of each of the TINKER potential energy
programs.Adetailedexampleshowinghowtoruneachprogramisincludedinalatersection.The
programs listed below are all part of the main, supported distribution. Additional source code for
variousunsupportedprogramscanbefoundinthe/otherdirectoryoftheTINKERdistribution.
ALCHEMY
A simple program to perform very basic free energy perturbation calculations. This program is
provided mostly for demonstration purposes. For example, we use ALCHEMY in a molecular
modeling course laboratory exercise to perform such classic mutations as chloride to bromide and
ethanetomethanolinwater.Thepresentversionusestheperturbationformulaandwindowingwith
anexplicitmappingofatomsinvolvedinthemutation(``AMBER''-style),insteadofthermodynamic
integrationandindependentfreelypropagatinggroupsofmutatedatoms(``CHARMM''-style).Some
ofthecodespecifictothisprogramislimitedtotheAMBERandOPLSpotentialfunctionalforms,but
could be easily generalized to handle other potentials. A more general and sophisticated version is
currentlyunderdevelopment.
ANALYZE
Provides information about a specific molecular structure. The program will ask for the name of a
structure file, which must be in the TINKER .xyz file format, and the type of analysis desired.
Options allow output of: (1) total potential energy of the system, (2) breakdown of the energy by
potentialfunctiontypeoroverindividualatoms,(3)computationofthetotaldipolemomentandits
components,momentsofinertiaandradiusofgyration,(4)listingoftheparametersusedtocompute
selectedinteractionenergies,(5)energiesassociatedwithspecifiedindividualinteractions.
ANNEAL
Performs a molecular dynamics simulated annealing computation. The program starts from a
specifiedinputmolecularstructureinTINKER.xyzformat.Thetrajectoryisupdatedusingeithera
modifiedBeemanoravelocityVerletintegrationmethod.Theannealingprotocolisimplementedby
allowing smooth changes between starting and final values of the system temperature via the
Groningenmethodofcouplingtoanexternalbath.Thescalingcanbelinearorsigmoidalinnature.In
addition, parameters such as cutoff distance can be transformed along with the temperature. The
usermustinputthedesirednumberofdynamicsstepsforboththeequilibrationandcoolingphases,
atimeintervalforthedynamicssteps,andanintervalbetweencoordinate/trajectorysaves.Allsaved
coordinatesetsalongthetrajectoryareplacedinsequentiallynumberedcyclefiles.
DYNAMIC
Performsamoleculardynamics(MD)orstochasticdynamics(SD)computation.Startseitherfroma
specifiedinputmolecularstructure(an.xyzfile)orfromastructure-velocity-accelerationsetsaved
from a previous dynamics trajectory (a restart from a .dyn file). MD trajectories are propagated
usingeitheramodifiedBeemanoravelocityVerletintegrationmethod.SDisimplementedviaour
ownderivationofavelocityVerlet-basedalgorithm.Inadditiontheprogramcanperformfullcrystal
calculations,andcanoperateinconstantenergymodeorwithmaintenanceofadesiredtemperature
and/orpressureusingtheGroningenmethodofcouplingtoexternalbaths.Theusermustinputthe
desirednumberofdynamicssteps,atimeintervalforthedynamicssteps,andanintervalbetween
coordinate/trajectory saves. Coordinate sets along the trajectory can be saved as sequentially
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numberedcyclefilesordirectlytoaTINKERarchive.arcfile.Atthesametimethatapointalong
thetrajectoryissaved,thecompleteinformationneededtorestartthetrajectoryfromthatpointis
updatedandstoredinthe.dynfile.
GDA
A program to implement Straub's Gaussian Density Annealing algorithm over an effective series of
analytically smoothed potential energy surfaces. This method can be viewed as an extended
stochastic version of the diffusion equation method of Scheraga, et al., and also has many similar
features to the TINKER Potential Smoothing and Search (PSS) series of programs. The current
versionofGDAissimilartobutdoesnotexactlyreproduceStraub'spublishedmethodandislimited
to argon clusters and other simple systems involving only van der Waals interactions; further
modificationanddevelopmentofthiscodeiscurrentlyunderwayinthePonderresearchgroup.As
withotherprogramsinvolvingpotentialsmoothing,GDAcurrentlyrequiresuseofthesmooth.prm
forcefieldparameters.
MINIMIZE
TheMINIMIZEprogramperformsalimitedmemoryL-BFGSminimizationofaninputstructureover
Cartesian coordinates using a modified version of the algorithm of Jorge Nocedal. The method
requires only the potential energy and gradient at each step along the minimization pathway. It
requires storage space proportional to the number of atoms in the structure. The MINIMIZE
procedureisrecommendedforpreliminaryminimizationoftrialstructurestoanrmsgradientof1.0
to 0.1 kcal/mole/≈. It has a relatively fast cycle time and is tolerant of poor initial structures, but
converges in a slow, linear fashion near the minimum. The user supplies the name of the TINKER
.xyz coordinates file and a target rms gradient value at which the minimization will terminate.
Output consists of minimization statistics written to the screen or redirected to an output file, and
thenewcoordinateswrittentoupdated.xyzfilesortocyclefiles.
MINIROT
The MINIROT program uses the same limited memory L-BFGS method as MINIMIZE, but performs
thecomputationintermsofdihedralanglesinsteadofCartesiancoordinates.Outputissavedinan
updated.intfileorincyclefiles.
MINRIGID
TheMINRIGIDprogramissimilartoMINIMIZEexceptthatitoperatesonrigidbodiesstartingfroma
TINKER.xyzcoordinatefileandtherigidbodygroupdefinitionsfoundinthecorresponding.key
file.Outputissavedinanupdated.xyzfileorincyclefiles.
MONTE
The MONTE program implements the Monte Carlo Minimization algorithm developed by Harold
Scheraga's group and others. The procedure takes Monte Carlo steps for either a single atom or a
single torsional angle, then performs a minimization before application of the Metropolis sampling
method. This results in effective sampling of a modified potential surface where the only possible
energylevelsarethoseoflocalminimaontheoriginalsurface.Theprogramcanbeeasilymodifiedto
elaborateontheavailablemoveset.
NEWTON
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A truncated Newton minimization method which requires potential energy, gradient and Hessian
information.ThisprocedurehassignificantadvantagesoverstandardNewtonmethods,andisable
to minimize very large structures completely. Several options are provided with respect to
minimization method and preconditioning of the Newton equations. The default options are
recommendedunlesstheuserisfamiliarwiththemathinvolved.ThisprogramoperatesinCartesian
coordinatespaceandisfairlytolerantofpoorinputstructures.Typicalalgorithmiterationtimesare
longerthanwithnonlinearconjugategradientorvariablemetricmethods,butmanyfeweriterations
arerequiredforcompleteminimization.NEWTONisusuallythebestchoiceforminimizationstothe
0.01 to 0.000001 kcal/mole/≈ level of rms gradient convergence. Tests for directions of negative
curvature can be removed, allowing NEWTON to be used for optimization to conformational
transitionstatestructures(thisonlyworksifthestartingpointisveryclosetothetransitionstate).
InputconsistsofaTINKER.xyzcoordinatesfile;outputisanupdatedsetofminimizedcoordinates
andminimizationstatistics.
NEWTROT
TheNEWTROTprogramissimilartoNEWTONexceptthatitrequiresa.intfileasinputandthen
operatesintermsofdihedralanglesastheminimizationvariables.SincethedihedralspaceHessian
matrixofanarbitrarystructureisoftenindefinite,thismethodwilloftennotperformaswellasthe
other,simplerdihedralanglebasedminimizers.
OPTIMIZE
TheOPTIMIZEprogramperformsaoptimallyconditionedvariablemetricminimizationofaninput
structure over Cartesian coordinates using an algorithm due to William Davidon. The method does
notperformlinesearches,butrequirescomputationofenergiesandgradientsaswellasstoragefor
an estimate of the inverse Hessian matrix. The program operates on Cartesian coordinates from a
TINKER .xyz file. OPTIMIZE will typically converge somewhat faster and more completely than
MINIMIZE.However,theneedtostoreandmanipulateafullinverseHessianestimatelimitsitsuseto
structures containing less than a few hundred atoms on workstation class machines. As with the
other minimizers, OPTIMIZE needs input coordinates and an rms gradient cutoff criterion. The
outputcoordinatesaresavedinupdated.xyzfilesorascyclefiles.
OPTIROT
The OPTIROT program is similar to OPTIMIZE except that it operates on dihedral angles starting
fromaTINKER.intinternalcoordinatefile.Thisprogramisusuallythepreferredmethodformost
dihedralangleoptimizationproblemssinceTruncatedNewtonmethodsappear,inourhands,tolose
someoftheirefficacyinmovingfromCartesiantotorsionalcoordinates.
OPTRIGID
TheOPTRIGIDprogramissimilartoOPTIMIZEexceptthatitoperatesonrigidbodiesstartingfroma
TINKER.xyzcoordinatefileandtherigidbodyatomgroupdefinitionsfoundinthecorresponding
.keyfile.Outputissavedinanupdated.xyzfileorincyclefiles.
PATH
AprogramthatimplementsavariantofElber'sLagrangianmultiplier-basedreactionpathfollowing
algorithm. The program takes as input a pair of structural minima as TINKER .xyz files, and then
generatesauserspecifiednumberofpointsalongapaththroughconformationalspaceconnecting
the input structures. The intermediate structures are output as TINKER cycle files, and the higher
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energyintermediatescanbeusedasinputtoaNewton-basedoptimizationtolocateconformational
transitionstates.
PSS
Implementsourversionofapotentialsmoothingandsearchalgorithmfortheglobaloptimizationof
molecular conformation. An initial structure in .xyz format is first minimized in Cartesian
coordinates on a series of increasingly smoothed potential energy surfaces. Then the smoothing
procedureisreversedwithminimizationoneachsuccessivesurfacestartingfromthecoordinatesof
the minimum on the previous surface. A local search procedure is used during the backtracking to
exploreforalternativeminimabetterthantheonefoundduringthecurrentminimization.Thefinal
resultisusuallyaverylowenergyconformationor,infavorablecases,theglobalenergyminimum
conformation.Theminimumenergycoordinatesetsfoundoneachsurfaceduringboththeforward
smoothingandbacktrackingproceduresareplacedinsequentiallynumberedcyclefiles.
PSSRIGID
ThisprogramimplementsthepotentialsmoothingandsearchmethodasdescribedaboveforthePSS
program,butperformsthecomputationintermsofkeyfile-definedrigidbodyatomgroupsinsteadof
Cartesiancoordinates.Outputissavedinnumberedcyclefileswiththe.xyzfileformat.
PSSROT
ThisprogramimplementsthepotentialsmoothingandsearchmethodasdescribedaboveforthePSS
program,butperformsthecomputationintermsofasetofuser-specifieddihedralanglesinsteadof
Cartesiancoordinates.Outputissavedinnumberedcyclefileswiththe.intfileformat.
SADDLE
A program for the location of a conformational transition state between two potential energy
minima. SADDLE uses a conglomeration of ideas from the Bell-Crighton quadratic path and the
Halgren-Lipscombsynchronoustransitmethods.Thebasicideaistoperformanonlinearconjugate
gradient optimization in a subspace orthogonal to a suitably defined reaction coordinate. The
program requires as input the coordinates (TINKER .xyz files) of the two minima and an rms
gradient convergence criterion for the optimization. The current estimate of the transition state
structureiswrittentothefileTSTATE.XYZ.CrudetransitionstatestructuresgeneratedbySADDLE
can sometimes be refined using the NEWTON program. Optionally, a scan of the interconversion
pathwaycanbemadeateachmajoriteration.
SCAN
A program for general conformational search of an entire potential energy surface via a basin
hopping method. The program takes as input a TINKER .xyz coordinates file which is then
minimized to find the first local minimum for a search list. A series of activations along various
normal modes from this initial minimum are used as seed points for additional minimizations.
Whenever a previously unknown local minimum is located it is added to the search list. When all
minima on the search list have been subjected to the normal mode activation without locating
additional new minima, the program terminates. The individual local minima are written to cycle
filesastheyarediscovered.WhiletheSCANprogramcanbeusedonstandardundeformedpotential
energy surfaces, we have found it to be most useful for quickly ``scanning'' a smoothed energy
surfacetoenumeratethemajorbasinsofattractionspaningtheentiresurface.
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SNIFFER
A program that implements the Sniffer global optimization algorithm of Butler and Slaminka, a
discreteversionofGriewank'sglobalsearchtrajectorymethod.TheprogramtakesaninputTINKER
.xyzcoordinatesfileandshakesitvigorouslyviaamodifieddynamicstrajectorybefore,hopefully,
settling into a low lying minimum. Some trial and error is often required as the current
implementation is sensitive to various parameters and tolerances that govern the computation. At
present,theseparametersarenotuseraccessible,andmustbealteredinthesourcecode.However,
this method can do a good job of quickly optimizing conformation within a limited range of
convergence.
TESTGRAD
TheTESTGRADprogramcomputesandcomparestheanalyticalandnumericalfirstderivatives(i.e.,
the gradient vector) of the potential energy for a Cartesian coordinate input structure. The output
canbeusedtotestordebugthecurrentpotentialoranyaddeduserdefinedenergyterms.
TESTHESS
The TESTHESS program computes and compares the analytical and numerical second derivatives
(i.e., the Hessian matrix) of the potential energy for a Cartesian coordinate input structure. The
outputcanbeusedtotestordebugthecurrentpotentialoranyaddeduserdefinedenergyterms.
TESTLIGHT
A program to compare the efficiency of different nonbonded neighbor methods for the current
molecularsystem.TheprogramtimesthecomputationofenergyandgradientforthevanderWaals
andcharge-chargeelectrostaticpotentialtermsusingasimpledoubleloopoverallinteractionsand
usingtheMethodofLightsalgorithmtoselectneighbors.Theresultscanbeusedtodecidewhether
theMethodofLightshasanyCPUtimeadvantageforthecurrentstructure.Bothmethodsshouldgive
exactlythesameanswerinallcases,sincetheidenticalindividualinteractionsarecomputedbyboth
methods. The default double loop method is faster when cutoffs are not used, or when the cutoff
spherecontainsabouthalformoreofthetotalsystemofunitcell.Incaseswherethecutoffsphereis
much smaller than the system size, the Method of Lights can be much faster since it avoids
unnecessarycalculationofdistancesbeyondthecutoffrange.
TESTROT
The TESTROT program computes and compares the analytical and numerical first derivatives (i.e.,
thegradientvector)ofthepotentialenergywithrespecttodihedralangles.InputisaTINKER.int
internal coordinate file. The output can be used to test or debug the current potential functions or
anyaddeduserdefinedenergyterms.
TIMER
AsimpleprogramtoprovidetimingstatisticsforenergyfunctioncallswithintheTINKERpackage.
TIMER requires an input .xyz file and outputs the CPU time (wall clock time on some machine
types)neededtoperformaspecifiednumberofenergy,gradientandHessianevaluations.
TIMEROT
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ThisprogramissimilartoTIMER,onlyitoperatesoverdihedralanglesviainputofaTINKER.int
internalcoordinatefile.Inthecurrentversion,thetorsionalHessianiscomputednumericallyfrom
theanalyticaltorsionalgradient.
VIBRATE
A program to perform vibrational analysis by computing and diagonalizing the full Hessian matrix
(i.e., the second partial derivatives) for an input structure (a TINKER .xyz file). Eigenvalues and
eigenvectorsofthemassweightedHessian(i.e.,thevibrationalfrequenciesandnormalmodes)are
alsocalculated.Structurescorrespondingtoindividualnormalmodemotionscanbesavedincycle
files.
VIBROT
The program VIBROT forms the torsional Hessian matrix via numerical differentiation of the
analytical torsional gradient. The Hessian is then diagonalized and the eigenvalues are output. The
presentversiondoesnotcomputethekineticenergymatrixelementsneededtoconverttheHessian
intothetorsionalnormalmodes;thiswillbeaddedinalaterversion.TherequiredinputisaTINKER
.intinternalcoordinatefile.
XTALFIT
TheXTALFITprogramisofuseintheautomatedfittingofpotentialparameterstocrystalstructure
andthermodynamicdata.XTALFITtakesasinputseveralcrystalstructures(TINKER.xyzfileswith
unitcellparametersincorrespondingkeyfiles)aswellasinformationonlatticeenergiesanddipole
momentsofmonomers.Thecurrentversionusesanonlinearleastsquaresoptimizationtofitvander
Waals and electrostatic parameters to the input data. Bounds can be placed on the values of the
optimizationparameters.
XTALMIN
A program to perform full crystal minimizations. The program takes as input the structure
coordinatesandunitcelllatticeparameters.ItthenalternatescyclesofNewton-styleoptimizationof
thestructureandconjugategradientoptimizationofthecrystallatticeparameters.Thisalternating
minimization is slower than more direct optimization of all parameters at once, but is somewhat
morerobustinourhands.Thesymmetryoftheoriginalcrystalisnotenforced,sointerconversionof
crystalformsmaybeobservedinsomecases.
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5.
AdditionalUtilityPrograms&Scripts
ThissectionofthemanualcontainsabriefdescriptionofeachoftheTINKERstructuremanipulation,
geometriccalculationandauxiliaryprograms.Adetailedexampleshowinghowtoruneachprogram
is included in a later section. The programs listed below are all part of the main, supported
distribution. Additional source code for various unsupported programs can be found in the /other
directoryoftheTINKERdistribution.
ARCHIVE
A program for concatenating TINKER cycle files into a single archive file; useful for storing the
intermediate results of minimizations, dynamics trajectories, and so on. The archive file can be
written in TINKER format, or in formats usable with MSI's InsightII (their CAR file with .msi
extension)orwithXMakemol(theirfileformatwith.xmolextension).Onlyactiveatomsarewritten
intotheInsightIIandXMakemoloutputfiles,allowingdisplayofpartialstructures.Theprogramcan
alsoextractindividualcyclefilesfromaTINKERarchive.
CORRELATE
A program to compute time correlation functions from collections of TINKER cycle files. Its use
requiresausersuppliedfunctionpropertythatcomputesthevalueofthepropertyforwhichatime
correlationisdesiredfortwoinputstructures.Asampleroutineissuppliedthatcomputeseithera
velocityautocorrelationfunctionoranrmsstructuralsuperpositionasafunctionoftime.Themain
bodyoftheprogramorganizestheoverallcomputationinanefficientmannerandoutputsthefinal
timecorrelationfunction.
CRYSTAL
A program for the manipulation of crystal structures including interconversion of fractional and
Cartesian coordinates, generation of the unit cell from an asymmetric unit, and building of a
crystallineblockofspecifiedsizeviareplicationofasingleunitcell.Thepresentversioncanhandle
about25ofthemostcommonspacegroups,otherscaneasilybeaddedasneededbymodificationof
theroutinesymmetry.
DIFFUSE
Aprogramtocomputetheself-diffusionconstantforahomogeneousliquidviatheEinsteinequation.
Apreviouslysaveddynamicstrajectoryisreadinand``unfolded''toreversetranslationofmolecules
due to use of periodic boundary conditions. The average motion over all molecules is then used to
compute the self-diffusion constant. While the current program assumes a homogeneous system, it
shouldbeeasytomodifythecodetohandlediffusionofindividualmoleculesorotherdesiredeffects.
DISTGEOM
A program to perform distance geometry calculations using variations on the classic metric matrix
method. A user specified number of structures consistent with keyfile input distance and dihedral
restraintsisgenerated.Bondlengthandanglerestraintsarederivedfromtheinputstructure.Trial
distancesbetweenthetrianglesmoothedlowerandupperboundscanbechosenviaanyofseveral
metrizationmethods,includingaveryeffectivepartialrandompairwisescheme.Thecorrectradius
of gyration of the structure is automatically maintained by choosing trial distances from Gaussian
distributionsofappropriatemeanandwidth.Theinitialembeddedstructurescanbefurtherrefined
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against a geometric restraint-only potential using either a sequential minimization protocol or
simulatedannealing.
DOCUMENT
TheDOCUMENTprogramisprovidedasaminimallistinganddocumentationtool.Itoperatesonthe
TINKERsourcecode,eitherindividualfilesorthecompletesourcelistingproducedbythecommand
scriptlisting.make,togeneratelistsofroutines,commonblocksorvalidkeywords.Inaddition,
the program has the ability to output a formatted parameter listing from the standard TINKER
parameterfiles.
INTEDIT
A program to allow interactive inspection and alteration of the internal coordinate definitions and
valuesofaTINKERstructure.Ifthestructureisaltered,theuserhastheoptiontowriteoutanew
internalcoordinatesfileuponexit.
INTXYZ
A program to convert a TINKER .int internal coordinates formatted file into a TINKER .xyz
Cartesiancoordinatesformattedfile.
NUCLEIC
Aprogramforautomatedbuildingofnucleicacidstructures.Uponinteractiveinputofanucleotide
sequence with optional phosphate backbone angles, the program builds internal and Cartesian
coordinates. Standard bond lengths and angles are used. Both DNA and RNA sequences are
supported as are A-, B- and Z-form structures. Double helixes of complementary sequence can be
automaticallyconstructedviaarigiddockingofindividualstrands.
PDBXYZ
A program for converting a Brookhaven Protein Data Bank file (a PDB file) into a TINKER .xyz
Cartesian coordinate file. If the PDB file contains only protein/peptide amino acid residues, then
standardproteinconnectivityisassumed,andtransferredtothe.xyzfile.Fornon-proteinportionsof
the PDB file, atom connectivity is determined by the program based on interatomic distances. The
program also has the ability to add or remove hydrogen atoms from a protein as required by the
forcefieldspecifiedduringthecomputation.
POLARIZE
A program for computing molecular polarizability from an atom-based distributed model of
polarizability.AdampedinteractionmodelduetoTholeisoptionallyviakeyfilesettings.ATINKER
.xyz file is required as input. The output consists of the overall polarizability tensor in the global
coordinatesanditseigenvalues.
PRMEDIT
AprogramforformattingandrenumberingTINKERforcefieldparameterfiles.Whenatomtypesor
classes are added to a parameter file, this utility program has the ability to renumber all the atom
records sequentially, and alter type and class numbers in all other parameter entries to maintain
consistency.
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PROTEIN
A program for automated building of peptide and protein structures. Upon interactive input of an
aminoacidsequencewithoptionalphi/psi/omega/chiangles,D/Lchirality,etc.,theprogrambuilds
internal and Cartesian coordinates. Standard bond lengths and angles are assumed for the peptide.
Theprogramwilloptionallyconvertthestructuretoacyclicpeptide,oraddeitherorbothN-andCterminalcappinggroups.Atomtypenumbersareautomaticallyassignedforthespecifiedforcefield.
Thefinalcoordinatesandasequencefileareproducedastheoutput.
RADIAL
A program to compute the pair radial distribution function between two atom types. The user
suppliesthetwoatomnamesforwhichthedistributionfunctionistobecomputed,andthewidthof
thedistancebinsfordataanalysis.Apreviouslysaveddynamicstrajectoryisreadasinput.Theraw
radial distribution and a spline smoothed version are then output from zero to a distance equal to
halftheminimumperiodicboxdimension.Theatomnamesarematchedtotheatomnamecolumnof
theTINKER.xyzfile,independentofatomtype.
SPACEFILL
A program to compute the volume and surface areas of molecules. Using a modified version of
Connolly'soriginalanalyticaldescriptionofthemolecularsurface,theprogramdetermineseitherthe
van der Waals, accessible or molecular (contact/reentrant) volume and surface area. Both surface
areaandvolumearebrokendownintotheirgeometriccomponents,andsurfaceareaisdecomposed
intotheconvexcontributionforeachindividualatom.Theproberadiusisinputasauseroption,and
atomicradiicanbesetviathekeywordfile.IfTINKERarchivefilesareusedasinput,theprogram
willcomputethevolumeandsurfaceareaofeachstructureintheinputfile.
SPECTRUM
Aprogramtocomputeapowerspectrumfromvelocityautocorrelationdata.Asinput,thisprogram
requires a velocity autocorrelation function as produced by the CORRELATE program. This data,
alongwithauserinputtimestep,areFouriertransformedtogeneratethespectralintensitiesovera
wavelengthrange.Theresultisapowerspectrum,andthepositionsofthebandsarethosepredicted
foraninfraredorRamanspectrum.However,thedataisnotweightedbymoleculardipolemoment
derivativesaswouldberequiredtoproducecorrectIRintensities.
SUPERPOSE
Aprogramtosuperimposetwomolecularstructuresin3-dimensions.Avarietyofoptionsforinput
of the atom sets to be used during the superposition are presented interactively to the user. The
superposition can be mass-weighted if desired, and the coordinates of the second structure
superimposedonthefirststructureareoptionallyoutput.IfTINKERarchivefilesareusedasinput,
theprogramwillcomputeallpairwisesuperpositionsbetweenstructuresintheinputfiles.
SYBYLXYZ
A program for converting a TRIPOS Sybyl MOL2 file into a TINKER .xyz Cartesian coordinate file.
ThecurrentversionoftheprogramdoesnotattempttoconverttheSybylatomstypesintotheactive
TINKERforcefieldtypes,i.e.,allatomstypesaresimplysettozero.
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XYZEDIT
A program that performs and of a variety of manipulations on an input TINKER .xyz Cartesian
coordinates formatted file. The present version of the program has the following interactively
selectableoptions:(1)OffsettheNumbersoftheCurrentAtoms,(2)DeletionofIndividualSpecified
Atoms, (3) Deletion of Specified Types of Atoms, (4) Deletion of Atoms outside Cutoff Range, (5)
Insertion of Individual Specified Atoms, (6) Replace Old Atom Type with a New Type, (7) Assign
ConnectivitiesbasedonDistance,(8)ConvertUnitsfromBohrstoAngstroms,(9)InvertthruOrigin
togiveMirrorImage,(10)TranslateCenterofMasstotheOrigin,(11)TranslateaSpecifiedAtomto
the Origin, (12) Translate and Rotate to Inertial Frame, (13) Move to Specified Rigid Body
Coordinates, (14) Create and Fill a Periodic Boundary Box, (15) Soak Current Molecule in Box of
Solvent,(16)AppendanotherXYZfiletoCurrentOne.Inmostcases,multiplyoptionscanbeapplied
sequentiallytoaninputfile.Attheendoftheeditingprocess,anewversionoftheoriginal.xyzfile
iswrittenasoutput.
XYZINT
AprogramforconvertingaTINKER.xyzCartesiancoordinateformattedfileintoaTINKER.int
internalcoordinatesformattedfile.Thisprogramcanoptionallyuseanexistinginternalcoordinates
fileasatemplatefortheconnectivityinformation.
XYZPDB
AprogramforconvertingaTINKER.xyzCartesiancoordinatefileintoaBrookhavenProteinData
Bankfile(aPDBfile).
XYZSYBYL
AprogramtoconvertaTINKER.xyzCartesiancoordinatesfileintoaTRIPOSSybylMOL2file.The
conversion generates only the MOLECULE, ATOM, BOND and SUBSTRUCTURE record type in the
MOL2file.GenericSybylatomtypesareusedinmostcases;whiletheseatomtypesmayneedtobe
alteredinsomecases,SybylisusuallyabletocorrectlydisplaytheresultingMOL2file.
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6.
SpecialFeatures&Methods
This section contains several short notes with further information about TINKER methodology,
algorithmsandspecialfeatures.Thediscussionisnotintendedtobeexhaustive,butrathertoexplain
featuresandcapabilitiessothatuserscanmakemorecompleteuseofthepackage.
FileVersionNumbers
AlloftheinputandoutputfiletypesroutinelyusedbytheTINKERpackagearecapableofexistingas
multiple versions of a base file name. For example, if the program XYZINT is run on the input file
molecule.xyz, the output internal coordinates file will be written to molecule.int. If a file
namedmolecule.intisalreadypresentpriortorunningXYZINT,thentheoutputwillbewritten
insteadtothenextavailableversion,inthiscasetomolecule.int_2.Infacttheoutputisgenerally
written to the lowest available, previously unused version number (molecule.int_3,
molecule.int_4, etc., as high as needed). Input file names are handled similarly. If simply
molecule or molecule.xyz is entered as the input file name upon running XYZINT, then the
highestversionofmolecule.xyzwillbeusedastheactualinputfile.Ifanexplicitversionnumber
isenteredaspartoftheinputfilename,thenthespecifiedversionwillbeusedastheinputfile.
The version number scheme will be recognized by many older users as a holdover from the VMS
originsofthefirstversionoftheTINKERsoftware.Ithasbeenmaintainedtomakeiteasiertochain
together multiple calculations that may create several new versions of a given file, and to make it
more difficult to accidently overwrite a needed result. The version scheme applies to most uses of
many common TINKER file types such as .xyz, .int, .key, .arc. It is not used when an
overwrittenfile``update''isobviouslythecorrectaction,forexample,the.dynmoleculardynamics
restart files. For those users who prefer a more Unix-like operation, and do not desire use of file
versions,thisfeaturecanbeturnedoffbyaddingtheNOVERSIONkeywordtotheapplicableTINKER
keyfile.
The version scheme as implemented in TINKER does have two known quirks. First, it becomes
impossible to directly use the original unversioned copy of a file if higher version numbers are
present. For example, if the files molecule.xyz and molecule.xyz_2 both exist, then
molecule.xyzcannotbeaccessedasinputbyXYZINT.Ifmolecule.xyzisenteredinresponseto
the input file name question, molecule.xyz_2 (or the highest present version number) will be
used as input. The only workaround is to copy or rename molecule.xyz to something else, say
molecule.new,andusethatnamefortheinputfile.Secondly,missingversionnumbersalwaysend
the search for the highest available version number; i.e., version numbers are assumed to be
consecutive and without gaps. For example, if molecule.xyz, molecule.xyz_2 and
molecule.xyz_4arepresent,butnotmolecule.xyz_3,thenmolecule.xyz_2willbeusedas
inputtoXYZINTifmoleculeisgivenastheinputfilename.Similarly,outputfileswillfillingapsin
analreadyexistingsetoffileversions.
CommandLineOptions
Manyoperatingsystemsorcompilersupplied-librariesmakeavailablesomethinglikethestandard
Unix iargc and getarg routines for capturing command line arguments. On these machines most of
theTINKERprogramssupportaselectionofcommandlineargumentsandoptions.Thenameofthe
keyfiletobeusedforacalculationisreadfromtheargumentfollowinga-k(equivalenttoeitherkeyor-keyfile,caseinsensitive)commandlineargument.Notethatthe-koptionscanappear
anywhereonthecommandlinefollowingtheexecutablename.Allothercommandlinearguments,
excepting the name of the executable program itself, are treated as input arguments. These input
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argumentsarereadfromlefttorightandinterpretedinorderastheanswerstoquestionsthatwould
be asked by an interactive invocation of the same TINKER program. For example, the following
commandline:
newton molecule -k test a a 0.01
willinvoketheNEWTONprogramonthestructurefilemolecule.xyzusingthekeyfiletest.key,
automaticmode[a]forboththemethodandpreconditioning,and0.01fortheRMSgradientper
atom termination criterion in kcal/mole/≈. Provided that the force field parameter set, etc. is
provided in test.key, the above compuation will procede directly from the command line
invocationwithoutfurtherinteractiveinput.
UseonMicrosoftWindowsSystems
TINKER executables for Microsoft PC systems should be run from the DOS or Command Prompt
windowavailableunderthevariousversionsofWindows.TheTINKERexecutabledirectoryshould
beaddedtoyourpathviatheautoexec.batfileorsimilar.IfusingWin2000orXP,setthenumberof
scrollablelinesintheCommandPromptwindowtoaverylargenumber,sothatyouwillbeableto
inspect screen output after it flies by. With Win95/98, these Command Prompt windows are only
abletoscrollasmallnumberoflines(amazing!),soTINKERprogramswhichgeneratelargeamounts
ofscreenoutputshouldberunsuchthatoutputwillberedirectedtoafile.Thiscanbeaccomplished
by running the TINKER program in batch mode or by using the Unix-like output redirection build
intoDOS.Forexample,thecommand:
dynamic < molecule.inp > molecule.log
willruntheTINKERdynamicprogramtakinginputfromthefilemolecule.inpandsendingoutput
tomolecule.log.Alsonotethatcommandlineoptionsasdescribedaboveareavailablewiththe
distributedTINKERexecutables.
Anotheralternative,particularlyattractivetothosealreadyfamiliarwithLinuxorUnixsystems,isto
download the Cygwin package currently available under GPL license from the site
http://source.redhat.com/cygwin/. The cygwin tools provide many of the GNU tools,
includingabashshellwindowfromwhichTINKERprogramscanberun.
If the distributed TINKER executables are run directly from Windows by double clicking on the
program icon, then the program will run in its own window. However, upon completion of the
program the window will close and screen output will be lost. Any output files written by the
programwill,ofcourse,stillbeavailable.TheWindowsbehaviorcanbechangedbyaddingtheEXITPAUSE keyword to the keyfile. This keyword causes the executation window to remain open after
completionuntilthe``Enter''keyispressed.
UseonAppleMacintoshSystems
The TINKER executables are best run under Mac OS X in a ``terminal'' application window where
behaviorisidenticaltothatinaLinuxterminal.AtpresenttheForceFieldExplorerGUIforTINKER
willnotrunonOSXsincetherequiredJava3Dextensionsareunavailable.
WehavediscontinuedactivesupportforMacOS9.However,theOS9versionsofTINKERarerunby
double clicking on a program icon. The program will run in its own window to which all ``screen''
output will be directed. Upon program termination the window will remain active pending a final
returnenteredbytheuserwhichwillclosethewindow.Priortothefinalreturn,thecontentsofthe
screenwindowcanbesavedtoafileviatheclipboardforpermanentstorage.NotethatMacintosh
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TINKERUser'sGuide
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OS9usesacoloninsteadofaforward-orback-slashasthedirectoryseparator,sokeyfilestransfered
fromothermachineswillneedtobealteredaccordingly.
AtomTypesvs.AtomClasses
Manipulationofatomtypesandtheproliferationofparametersasatomsarefurthersubdividedinto
new types is the bane of force field calculation. For example, if each topologically distinct atom
arisingfromthe20naturalaminoacidsisgivenadifferentatomtype,thenabout300separatetype
are required (this ignores the different N- and C-terminal forms of the residues, diastereotopic
hydrogens, etc.). However, all these types lead to literally thousands of different force field
parameters.Infact,therearemanythousandsofdistincttorsionalparametersalone.Itisimpossible
at present to fully optimize each of these parameters; and even if we could, a great many of the
parameters would be nearly identical. Two somewhat complimentary solutions are available to
handle the proliferation of parameters. The first is to specify the molecular fragments to which a
given parameter can be applied in terms of a chemical structure language, SMILES strings for
example.Somecommercialsystems,suchastheTRIPOSSybylsoftware,makeuseofsuchascheme
toparsestructuresandassignforcefieldparameters.
A second general approach is to use hierarchical cascades of parameter groups. TINKER uses a
simpleversionofthisscheme.EachTINKERforcefieldatomhasbothanatomtypenumberandan
atom class number. The types are subsets of the atom classes, i.e., several different atom types can
belong to the same atom class. Force field parameters that are somewhat less sensitive to local
environment, such as local geometry terms, are then provided and assigned based on atom class.
Otherenergyparameters,suchaselectrostaticparameters,thatareveryenvironmentdependentare
assigned over the atom types. This greatly reduces the number of independent multiple-atom
parameterslikethefour-atomtorsionalparameters.
CalculationsonPartialStructures
Twomethodsareavailableforperformingenergeticcalculationsonportionsorsubstructureswithin
a full molecular system. TINKER allows division of the entire system into active and inactive parts
which can be defined via keywords. In subsequent calculations, such as minimization or dynamics,
only the active portions of the system are allowed to move. The force field engine responds to the
active/inactivedivisionbycomputingallenergeticinteractionsinvolvingatleastoneactiveatom;i.e.,
anyinteractionwhoseenergycanchangewiththemotionofoneormoreactiveatomsiscomputed.
Thesecondmethodforpartialstructurecomputationinvolvesdividingtheoriginalsystemintoaset
ofatomgroups.Asbefore,thegroupscanbespecifiedviaappropriatekeywords.ThecurrentTINKER
implementationallowsspecificationofuptoamaximumnumberofgroupsasgiveninthesizes.i
dimensioningfile.Thegroupsmustbedisjointinthatnoatomcanbelongtomorethanonegroup.
Furtherkeywordsallowtheusertospecifywhichintra-andintergroupsetsofenergeticinteractions
willcontributetothetotalforcefieldenergy.Weightsforeachsetofinteractionsinthetotalenergy
canalsobeinput.Aspecificenergeticinteractionisassignedtoaparticularintra-orintergroupsetif
all the atoms involved in the interaction belong to the group (intra-) or pair of groups (inter-).
Interactionsinvolvingatomsfrommorethantwogroupsarenotcomputed.
Note that the groups method and active/inactive method use different assignment procedures for
individualinteractions.Theactive/inactiveschemeisintendedforsituationswhereonlyaportionof
a system is allowed to move, but the total energy needs to reflect the presence of the remaining
inactive portion of the structure. The groups method is intended for use in rigid body calculations,
andisneededforcertainkindsoffreeenergyperturbationcalculations.
MetalComplexesandHypervalentSpecies
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ThedistributionversionofTINKERcomesdimensionedforamaximumatomiccoordinationnumber
of four as needed for standard organic compounds. In order to use TINKER for calculations on
speciescontaininghighercoordinationnumbers,simplychangethevalueoftheparametermaxval
in the master dimensioning file sizes.i and rebuilt the package. Note that this parameter value
shouldnotbesetlargerthannecessarysincelargevaluescanslowtheexecutionofportionsofsome
TINKERprograms.
Manymolecularmechanicsapproachestoinorganicandmetalstructuresuseananglebendingterm
which is softer than the usual harmonic bending potential. TINKER implements a Fourier bending
term similar to that used by the Landis group's SHAPES force field. The parameters for specific
FourierangletermsaresuppliedviatheANGLEFparameterandkeywordformat.NotethataFourier
termwillonlybeusedforaparticularangleifacorrespondingharmonicangletermisnotpresentin
theparameterfile.
WearenowcollaboratingwithAndersCarlsson'sgroupinSt.Louistoaddhistransitionmetalligand
fieldtermtoTINKER.SupportforthisadditionalpotentialfunctionalformisalreadyintheTINKER
sourcecode,andweplantoreleasetheenergyroutinesafterfurthertestingandparameterization.
NeighborMethodsforNonbondedTerms
In addition to standard double loop methods, the Method of Lights is available to speed neighbor
searching. This method based on taking intersections of sorted atom lists can be much faster for
problemswherethecutoffdistanceissignificantlysmallerthanhalfthemaximalcelldimension.The
currentversionofTINKERdoesnotimplementthe``neighborlist''schemescommontomanyother
simulationpackages.
PeriodicBoundaryConditions
Both spherical cutoff images or replicates of a cell are supported by all TINKER programs that
implementperiodicboundaryconditions.Wheneverthecutoffdistanceistoolargefortheminimum
imagetobetheonlyrelevantneighbor(i.e.,halftheminimumboxdimensionfororthogonalcells),
TINKERwillautomaticallyswitchfromtheimageformalismtouseofreplicatedcells.
DistanceCutoffsforEnergyFunctions
Polynomialenergyswitchingoverawindowisusedfortermswhoseenergyissmallnearthecutoff
distance.Formonopoleelectrostaticinteractions,whicharequitelargeintypicalcutoffranges,atwo
polynomial multiplicative-additive shifted energy switch unique to TINKER is applied. The TINKER
methodissimilarinspirittotheforceswitchingmethodsofSteinbachandBrooks,J.Comput.Chem.,
15, 667-683 (1994). While the particle mesh Ewald method is preferred when periodic boundary
conditionsarepresent,TINKER'sshiftedenergyswitchwithreasonableswitchingwindowsisquite
satisfactory for most routine modeling problems. The shifted energy switch minimizes the
perturbationoftheenergyandthegradientatthecutofftoacceptablelevels.Problemsshouldarise
only if the property you wish to monitor is known to require explicit inclusion of long range
components(i.e.,calculationofthedielectricconstant,etc.).
EwaldSummationsMethods
TINKER contains a versions of the Ewald summation technique for inclusion of long range
electrostatic interactions via periodic boundaries. The particle mesh Ewald (PME) method is
availableforsimplecharge-chargepotentials,whileregularEwaldisprovidedforpolarizableatomic
multipoleinteractions.TheaccuracyandspeedoftheregularandPMEcalculationsisdependenton
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several interrelated parameters. For both methods, the Ewald coefficient and real-space cutoff
distance must be set to reasonable and complementary values. Additional control variables for
regularEwaldarethefractionalcoverageandnumberofvectorsusedinreciprocalspace.ForPME
the additional control values are the B-spline order and charge grid dimensions. Complete control
overalloftheseparametersisavailableviatheTINKERkeyfilemechanism.BydefaultTINKERwill
selectasetofparameterswhichprovideareasonablecompromisebetweenaccuracyandspeed,but
theseshouldbecheckedandmodifiedasnecessaryforeachindividualsystem.
ContinuumSolvationModels
Several alternative continuum solvation algorithms are contained within TINKER. All of these are
accessed via the SOLVATE keyword and its modifiers. Two simple surface area methods are
implemented: the ASP method of Eisenberg and McLachlan, and the SASA method from Scheraga's
group. These methods are applicable to any of the standard TINKER force fields. Various schemes
based on the generalized Born formalism are also available: the original 1990 numerical ``Onionshell'' GB/SA method from Still's group, the 1997 analytical GB/SA method also due to Still, a
pairwise descreening algorithm originally proposed by Hawkins, Cramer and Truhlar, and the
analytical continuum solvation (ACE) method of Schaefer and Karplus. At present, the generalized
Born methods should only be used with force fields having simple partial charge electrostatic
interactions.
SomefurthercommentsareinorderregardingtheGB/SA-stylesolvationmodels.The``Onion-shell''
model is provided mostly for comparison purposes. It uses an exact, analytical surface area
calculation for the cavity term and the numerical scheme described in the original paper for the
polarization term. This method is very slow, especially for large systems, and does not contain the
contributionoftheBornradiichainruletermtothefirstderivatives.Werecommenditsuseonlyfor
single-point energy calculations. The other GB/SA methods (``analytical'' Still, H-C-T pairwise
descreening, and ACE) use an approximate cavity term based on Born radii, and do contain fully
correctderivativesincludingtheBornradiichainrulecontribution.ThesemethodsallscaleinCPU
time with the square of the size of the system, and can be used with minimization, molecular
dynamicsandlargemolecules.
Finally,wenotethattheACEsolvationmodelshouldnotbeusedwiththecurrentversionofTINKER.
The algorithm is fully implemented in the source code, but parameterization is not complete. As of
late 2000, parameter values are only available in the literature for use of ACE with the older
CHARMM19 force field. We plan to develop values for use with more modern all-atom force fields,
andthesewillbeincorporatedintoTINKERsometimeinthefuture.
PolarizableMultipoleElectrostatics
Atomicmultipoleelectrostaticsthroughthequadrupolemomentissupportedbythecurrentversion
of TINKER, as is either mutual or direct dipole polarization. Ewald summation is available for
inclusion of long range interactions. Calculations are implemented via a mixture of the CCP5
algorithms of W. Smith and the Applequist-Dykstra Cartesian polytensor method. At present
analyticalenergyandCartesiangradientcodeisprovided.
TheTINKERpackageallowsintramolecularpolarizationtobetreatedviaaversionoftheinteraction
dampingschemeofThole.ToimplementtheTholescheme,itisnecessarytosetallthemutual-1xscale keywords to a value of one. The other polarization scaling keyword series, direct-1xscale and polar-1x-scale, can be set independently to enable a wide variety of polarization
models. In order to use an Applequist-style model without polarization damping, simply set the
polar-dampkeywordtozero.
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PotentialEnergySmoothing
VersionsofourPotentialSmoothingandSearch(PSS)methodologyhavebeenimplementedwithin
TINKER.ThismethodsbelongtothesamegeneralfamilyasScheraga'sDiffusionEquationMethod,
Straub's Gaussian Density Annealing, Shalloway's Packet Annealing and Verschelde's Effective
Diffused Potential, but our algorithms reflect our own ongoing researchin this area. In many ways
the TINKER potential smoothing methods are the deterministic analog of stochastic simulated
annealing. The PSS algorithms are very powerful, but are relatively new and are still undergoing
modification,testingandcalibrationwithinourresearchgroup.ThisversionofTINKERalsoincludes
a basin-hopping conformational scanning algorithm in the program SCAN which is particularly
effectiveonsmoothedpotentialsurfaces.
DistanceGeometryMetrization
Amuchimprovedandveryfastrandompairwisemetrizationschemeisavailablewhichallowsgood
sampling during trial distance matrix generation without the usual structural anomalies and CPU
constraints of other metrization procedures. An outline of the methodology and its application to
NMRNOE-basedstructurerefinementisdescribedinthepaperbyHodsdon,etal.inJ.Mol.Biol.,264,
585-602 (1996). We have obtained good results with something like the keyword phrase trialdistribution pairwise 5, which performs 5% partial random pairwise metrization. For
structuresoverseveralhundredatoms,avaluelessthan5forthepercentageofmetrizationshould
befine.
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7.
UseoftheKeywordControlFile
UsingKeywordstoControlTINKERCalculations
Thissectioncontainsadescriptionoftheover300keywordparameterswhichmaybeusedtodefine
oralterthecourseofaTINKERcalculation.Thekeywordcontrolfileisoptionalinthesensethatall
of the TINKER programs will run in the absence of a keyfile and will simply use default values or
query the user for needed information. However, the keywords allow use of a wide variety of
algorithmicandproceduraloptions,manyofwhichareunavailableinteractively.
Keywordsarereadfromthekeywordcontrolfile.Allprogramslookfirstforakeyfilewiththesame
basenameastheinputmolecularsystemandendingintheextension.key.Ifthisfiledoesnotexist,
then TINKER tries to use a generic keyfile with the name tinker.key and located in the same
directory as the input system. If neither a system-specific nor a generic keyfile is present, TINKER
will continue by using default values for keyword options and asking interactive questions as
necessary.
TINKER searches the keyfile during the course of a calculation for relevant keywords that may be
present. All keywords must appear as the first word on the line. Any blank space to the left of the
keyword is ignored, and all contents of the keyfiles are case insensitive. Some keywords take
modifiers;i.e.,TINKERlooksfurtheronthesamelineforadditionalinformation,suchasthevalueof
some parameter related to the keyword. Modifier information is read in free format, but must be
completely contained on the same line as the original keyword. Any lines contained in the keyfile
whichdonotqualifyasvalidkeywordlinesaretreatedascommentsandaresimplyignored.
Several keywords take a list of integer values (atom numbers, for example) as modifiers. For these
keywordstheintegerscansimplybelistedexplicitlyandseparatedbyspaces,commasortabs.Ifa
range of numbers is desired, it can be specified by listing the negative of the first number of the
range, followed by a separator and the last number of the range. For example, the keyword line
ACTIVE 4 -9 17 23couldbeusedtoaddatoms4,9through17,and23tothesetofactiveatoms
duringaTINKERcalculation.
KeywordsGroupedbyFunctionality
ListedbelowaretheavailableTINKERkeywordssortedintogroupsbygeneralfunction.Thesection
endswithanalphabeticallistcontainingeachindividualkeyword,alongwithabriefdescriptionofits
action,possiblekeywordmodifiers,andusageexamples.
OUTPUTCONTROLKEYWORDS
ARCHIVE
ECHO
OVERWRITE
SAVE-FORCE
VERBOSE
DEBUG
EXIT-PAUSE
PRINTOUT
SAVE-INDUCED
WRITEOUT
DIGITS
NOVERSION
SAVE-CYCLE
SAVE-VELOCITY
FORCEFIELDSELECTIONKEYWORDS
FORCEFIELD
PARAMETERS
POTENTIALFUNCTIONSELECTIONKEYWORDS
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ANGANGTERM
ANGLETERM
CHARGETERM
CHGDPLTERM
EXTRATERM
IMPROPTERM
METALTERM
MPOLETERM
OPDISTTERM
PITORSTERM
RESTRAINTERM
RXNFIELDTERM
STRBNDTERM
STRTORTERM
TORTORTERM
UREYTERM
POTENTIALFUNCTIONPARAMETERKEYWORDS
BONDTERM
DIPOLETERM
IMPTORSTERM
OPBENDTERM
POLARIZETERM
SOLVATETERM
TORSIONTERM
VDWTERM
ANGANG
ANGLE4
ATOM
BOND3
CHARGE
DIPOLE4
HBOND
METAL
OPDIST
PITORS
STRBND
TORSION4
UREYBRAD
VDWPR
ANGLE3
ANGLEF
BOND
BOND5
DIPOLE3
ELECTNEG
IMPTORS
OPBEND
PIBOND
SOLVATE
TORSION
TORTOR
VDW14
ANGLE
ANGLE5
BIOTYPE
BOND4
DIPOLE
DIPOLE5
IMPROPER
MULTIPOLE
PIATOM
POLARIZE
STRTORS
TORSION5
VDW
ENERGYUNITCONVERSIONKEYWORDS
ANGLEUNIT
ELECTRIC
OPBENDUNIT
STRBNDUNIT
TORTORUNIT
ANGANGUNIT
IMPROPUNIT
OPDISTUNIT
STRTORUNIT
UREYUNIT
BONDUNIT
IMPTORUNIT
PITORSUNIT
TORSIONUNIT
LOCALGEOMETRYFUNCTIONALFORMKEYWORDS
ANGLE-CUBIC
ANGLE-SEXTIC
BONDTYPE
UREY-CUBIC
ANGLE-QUARTIC
BOND-CUBIC
MM2-STRBND
UREY-QUARTIC
ANGLE-PENTIC
BOND-QUARTIC
PISYSTEM
VANDERWAALSFUNCTIONALFORMKEYWORDS
A-EXPTERM
DELTA-HALGREN
GAUSSTYPE
RADIUSTYPE
VDW-14-SCALE
VDWINDEX
B-EXPTERM
EPSILONRULE
RADIUSRULE
VDW-12-SCALE
VDW-15-SCALE
VDWTYPE
C-EXPTERM
GAMMA-HALGREN
RADIUSSIZE
VDW-13-SCALE
VDW-CORRECTION
ELECTROSTATICSFUNCTIONALFORMKEYWORDS
CHG-12-SCALE
CHG-13-SCALE
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CHG-14-SCALE
30
CHG-15-SCALE
DIRECT-11-SCALE
DIRECT-14-SCALE
MPOLE-14-SCALE
MUTUAL-12-SCALE
POLAR-12-SCALE
POLAR-15-SCALE
POLAR-SOR
CHG-BUFFER
DIRECT-12-SCALE
MPOLE-12-SCALE
MPOLE-15-SCALE
MUTUAL-13-SCALE
POLAR-13-SCALE
POLAR-ASPC
POLARIZATION
DIELECTRIC
DIRECT-13-SCALE
MPOLE-13-SCALE
MUTUAL-11-SCALE
MUTUAL-14-SCALE
POLAR-14-SCALE
POLAR-EPS
REACTIONFIELD
CHG-TAPER
DPL-TAPER
MPOLE-CUTOFF
NEUTRAL-GROUPS
TRUNCATE
CUTOFF
HESS-CUTOFF
MPOLE-TAPER
POLYMER-CUTOFF
VDW-CUTOFF
EWALD-ALPHA
PME-GRID
EWALD-BOUNDARY
PME-ORDER
NONBONDEDCUTOFFKEYWORDS
CHG-CUTOFF
DPL-CUTOFF
LIGHTS
NEIGHBOR-GROUPS
TAPER
VDW-TAPER
EWALDSUMMATIONKEYWORDS
EWALD
EWALD-CUTOFF
CRYSTALLATTICE&PERIODICBOUNDARYKEYWORDS
A-AXIS
ALPHA
NO-SYMMETRY
X-AXIS
B-AXIS
BETA
OCTAHEDRON
Y-AXIS
C-AXIS
GAMMA
SPACEGROUP
Z-AXIS
LIST-BUFFER
VDW-LIST
MPOLE-LIST
CAPPA
INTMAX
NEWHESS
STEEPEST-DESCENT
FCTMIN
LBFGS-VECTORS
NEXTITER
STEPMAX
NEIGHBORLISTKEYWORDS
CHG-LIST
NEIGHBOR-LIST
OPTIMIZATIONKEYWORDS
ANGMAX
HGUESS
MAXITER
SLOPEMAX
STEPMIN
MOLECULARDYNAMICSKEYWORDS
BEEMAN-MIXING
REMOVE-INERTIA
DEGREES-FREEDOM
INTEGRATOR
THERMOSTAT&BAROSTATKEYWORDS
ANISO-PRESSURE
COMPRESS
TAU-PRESSURE
BAROSTAT
FRICTION
TAU-TEMPERATURE
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COLLISION
FRICTION-SCALING
THERMOSTAT
31
VOLUME-MOVE
VOLUME-SCALE
VOLUME-TRIAL
GAMMAMIN
REDUCE
TRANSITIONSTATEKEYWORDS
DIVERGE
SADDLEPOINT
DISTANCEGEOMETRYKEYWORDS
TRIAL-DISTANCE
TRIAL-DISTRIBUTION
VIBRATIONALANALYSISKEYWORDS
IDUMP
VIB-ROOTS
VIB-TOLERANCE
GK-RADIUS
SOLVENT-PRESSURE
GKC
SURFACE-TENSION
IMPLICITSOLVATIONKEYWORDS
BORN-RADIUS
GKR
POISSON-BOLTZMANNKEYWORDS
AGRID
CGCENT
FGRID
MG-MANUAL
SDENS
SRAD
APBS-GRID
CGRID
ION
PB-RADIUS
SDIE
SRFM
BCFL
FGCENT
MG-AUTO
PDIE
SMIN
SWIN
MATHEMATICALALGORITHMKEYWORDS
FFT-PACKAGE
RANDOMSEED
PARALLELIZATIONKEYWORDS
OPENMP-THREADS
FREEENERGYPERTURBATIONKEYWORDS
CHG-LAMBDA
LIGAND
POLAR-LAMBDA
DPL-LAMBDA
MPOLE-LAMBDA
VDW-LAMBDA
LAMBDA
MUTATE
GROUP
GROUP-MOLECULE
GROUP-INTER
GROUP-SELECT
PARTIALSTRUCTUREKEYWORDS
ACTIVE
GROUP-INTRA
INACTIVE
CONSTRAINT&RESTRAINTKEYWORDS
BASIN
RATTLE-DISTANCE
RATTLE-ORIGIN
ENFORCE-CHIRALITY
RATTLE-EPS
RATTLE-PLANE
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RATTLE
RATTLE-LINE
RESTRAIN-ANGLE
32
RESTRAIN-DISTANCE
RESTRAIN-TORSION
RESTRAIN-GROUPS
SPHERE
RESTRAIN-POSITION
WALL
FIT-BOND
FIT-TORSION
FIX-BOND
FIX-OPBEND
FIX-TORSION
POTENTIAL-FIT
POTENTIAL-SPACING
FIT-OPBEND
FIT-UREY
FIX-DIPOLE
FIX-QUADRUPOLE
FIX-UREY
POTENTIAL-OFFSET
TARGET-DIPOLE
PARAMETERFITTINGKEYWORDS
FIT-ANGLE
FIT-STRBND
FIX-ANGLE
FIX-MONOPOLE
FIX-STRBND
POTENTIAL-ATOMS
POTENTIAL-SHELLS
TARGET-QUADRUPOLE
POTENTIALSMOOTHINGKEYWORDS
DEFORM
DIFFUSE-VDW
DIFFUSE-CHARGE
SMOOTHING
DIFFUSE-TORSION
DescriptionofIndividualKeywords
The following is an alphabetical list of the TINKER keywords along with a brief description of the
action of each keyword and required or optional parameters that can be used to extend or modify
eachkeyword.Theformatofpossiblemodifiers,ifany,isshowninbracketsfollowingeachkeyword.
A-AXIS[real]Setsthevalueofthea-axislengthforacrystalunitcell,or,equivalently,theX-axis
lengthforaperiodicbox.ThelengthvalueinAngstromsislistedafterthekeyword.
A-EXPTERM[real]Setsthevalueofthe``A''premultipliertermintheBuckinghamvanderWaals
function,i.e.,thevalueofAintheformulaEvdw=ε{Aexp[-B(Ro/R)]-C(Ro/R)6}.
ACTIVE [integer list] Sets the list of active atoms during a TINKER computation. Individual
potential energy terms are computed when at least one atom involved in the term is active. For
Cartesian space calculations, active atoms are those allowed to move. For torsional space
calculations,rotationsareallowedwhenallatomsononesideoftherotatedbondareactive.Multiple
ACTIVElinescanbepresentinthekeyfileandaretreatedcumulatively.Oneachlinethekeyword
canbefollowedbyoneormoreatomnumbersoratomranges.ThepresenceofanyACTIVEkeyword
overridesanyINACTIVEkeywordsinthekeyfile.
ALPHA[real]Setsthevalueoftheαangleofacrystalunitcell,i.e.,theanglebetweentheb-axis
and c-axis of a unit cell, or, equivalently, the angle between the Y-axis and Z-axis of a periodic box.
ThedefaultvalueintheabsenceoftheALPHAkeywordis90degrees.
ANGANG [1 integer & 3 reals] This keyword provides the values for a single angle-angle cross
termpotentialparameter.
ANGANGTERM[NONE/ONLY]Thiskeywordcontrolsuseoftheangle-anglecrosstermpotential
energy.Intheabsenceofamodifyingoption,thiskeywordturnsonuseofthepotential.TheNONE
option turns off use of this potential energy term. The ONLY option turns off all potential energy
termsexceptforthisone.
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ANGANGUNIT [real] Sets the scale factor needed to convert the energy value computed by the
angle-angle cross term potential into units of kcal/mole. The correct value is force field dependent
andtypicallyprovidedintheheaderofthemasterforcefieldparameterfile.Thedefaultof(π/180)2
=0.0003046isused,iftheANGANGUNITkeywordisnotgivenintheforcefieldparameterfileorthe
keyfile.
ANGLE[3integers&4reals]Thiskeywordprovidesthevaluesforasinglebondanglebending
parameter.Theintegermodifiersgivetheatomclassnumbersforthethreekindsofatomsinvolved
intheanglewhichistobedefined.Therealnumbermodifiersgivetheforceconstantvalueforthe
angleanduptothreeidealbondanglesindegrees.Inmostcasesonlyoneidealbondangleisgiven,
and that value is used for all occurrences of the specified bond angle. If all three ideal angles are
given,thevaluesapplywhenthecentralatomoftheangleisattachedto0,1or2additionalhydrogen
atoms, respectively. This ``hydrogen environment'' option is provided to implement the
corresponding feature of Allinger's MM force fields. The default units for the force constant are
kcal/mole/radian2,butthiscanbecontrolledviatheANGLEUNITkeyword.
ANGLE-CUBIC[real]SetsthevalueofthecubictermintheTaylorseriesexpansionformofthe
bondanglebendingpotentialenergy.Therealnumbermodifiergivesthevalueofthecoefficientasa
multiple of the quadratic coefficient. This term multiplied by the angle bending energy unit
conversionfactor,theforceconstant,andthecubeofthedeviationofthebondanglefromitsideal
value gives the cubic contribution to the angle bending energy. The default value in the absence of
theANGLE-CUBICkeywordiszero;i.e.,thecubicanglebendingtermisomitted.
ANGLE-PENTIC[real]SetsthevalueofthefifthpowertermintheTaylorseriesexpansionformof
thebondanglebendingpotentialenergy.Therealnumbermodifiergivesthevalueofthecoefficient
as a multiple of the quadratic coefficient. This term multiplied by the angle bending energy unit
conversionfactor,theforceconstant,andthefifthpowerofthedeviationofthebondanglefromits
ideal value gives the pentic contribution to the angle bending energy. The default value in the
absenceoftheANGLE-PENTICkeywordiszero;i.e.,thepenticanglebendingtermisomitted.
ANGLE-QUARTIC[real]SetsthevalueofthequartictermintheTaylorseriesexpansionformof
thebondanglebendingpotentialenergy.Therealnumbermodifiergivesthevalueofthecoefficient
as a multiple of the quadratic coefficient. This term multiplied by the angle bending energy unit
conversionfactor,theforceconstant,andtheforthpowerofthedeviationofthebondanglefromits
ideal value gives the quartic contribution to the angle bending energy. The default value in the
absenceoftheANGLE-QUARTICkeywordiszero;i.e.,thequarticanglebendingtermisomitted.
ANGLE-SEXTIC[real]SetsthevalueofthesixthpowertermintheTaylorseriesexpansionformof
thebondanglebendingpotentialenergy.Therealnumbermodifiergivesthevalueofthecoefficient
as a multiple of the quadratic coefficient. This term multiplied by the angle bending energy unit
conversionfactor,theforceconstant,andthesixthpowerofthedeviationofthebondanglefromits
idealvaluegivesthesexticcontributiontotheanglebendingenergy.Thedefaultvalueintheabsence
oftheANGLE-SEXTICkeywordiszero;i.e.,thesexticanglebendingtermisomitted.
ANGLE3[3integers&4reals]Thiskeywordprovidesthevaluesforasinglebondanglebending
parameterspecifictoatomsin3-memberedrings.Theintegermodifiersgivetheatomclassnumbers
forthethreekindsofatomsinvolvedintheanglewhichistobedefined.Therealnumbermodifiers
givetheforceconstantvaluefortheangleanduptothreeidealbondanglesindegrees.Ifallthree
ideal angles are given, the values apply when the central atom of the angle is attached to 0, 1 or 2
additional hydrogen atoms, respectively. The default units for the force constant are
kcal/mole/radian2,butthiscanbecontrolledviatheANGLEUNITkeyword.IfanyANGLE3keywords
arepresent,eitherinthemasterforcefieldparameterfileorthekeyfile,thenTINKERrequiresthat
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special ANGLE3 parameters be given for all angles in 3-membered rings. In the absence of any
ANGLE3keywords,standardANGLEparameterswillbeusedforbondsin3-memberedrings.
ANGLE4[3integers&4reals]Thiskeywordprovidesthevaluesforasinglebondanglebending
parameterspecifictoatomsin4-memberedrings.Theintegermodifiersgivetheatomclassnumbers
forthethreekindsofatomsinvolvedintheanglewhichistobedefined.Therealnumbermodifiers
givetheforceconstantvaluefortheangleanduptothreeidealbondanglesindegrees.Ifallthree
ideal angles are given, the values apply when the central atom of the angle is attached to 0, 1 or 2
additional hydrogen atoms, respectively. The default units for the force constant are
kcal/mole/radian2,butthiscanbecontrolledviatheANGLEUNITkeyword.IfanyANGLE4keywords
arepresent,eitherinthemasterforcefieldparameterfileorthekeyfile,thenTINKERrequiresthat
special ANGLE4 parameters be given for all angles in 4-membered rings. In the absence of any
ANGLE4keywords,standardANGLEparameterswillbeusedforbondsin4-memberedrings.
ANGLE5[3integers&4reals]Thiskeywordprovidesthevaluesforasinglebondanglebending
parameterspecifictoatomsin5-memberedrings.Theintegermodifiersgivetheatomclassnumbers
forthethreekindsofatomsinvolvedintheanglewhichistobedefined.Therealnumbermodifiers
givetheforceconstantvaluefortheangleanduptothreeidealbondanglesindegrees.Ifallthree
ideal angles are given, the values apply when the central atom of the angle is attached to 0, 1 or 2
additional hydrogen atoms, respectively. The default units for the force constant are
kcal/mole/radian2,butthiscanbecontrolledviatheANGLEUNITkeyword.IfanyANGLE5keywords
arepresent,eitherinthemasterforcefieldparameterfileorthekeyfile,thenTINKERrequiresthat
special ANGLE5 parameters be given for all angles in 5-membered rings. In the absence of any
ANGLE5keywords,standardANGLEparameterswillbeusedforbondsin5-memberedrings.
ANGLEF[3integers&3reals]Thiskeywordprovidesthevaluesforasinglebondanglebending
parameter for a SHAPES-style Fourier potential function. The integer modifiers give the atom class
numbersforthethreekindsofatomsinvolvedintheanglewhichistobedefined.Therealnumber
modifiers give the force constant value for the angle, the angle shift in degrees, and the periodicity
value. Note that the force constant should be given as the ``harmonic'' value and not the native
Fourier value. The default units for the force constant are kcal/mole/radian2, but this can be
controlledviatheANGLEUNITkeyword.
ANGLETERM [NONE/ONLY] This keyword controls use of the bond angle bending potential
energy term. In the absence of a modifying option, this keyword turns on use of the potential. The
NONE option turns off use of this potential energy term. The ONLY option turns off all potential
energytermsexceptforthisone.
ANGLEUNIT[real]Setsthescalefactorneededtoconverttheenergyvaluecomputedbythebond
angle bending potential into units of kcal/mole. The correct value is force field dependent and
typically provided in the header of the master force field parameter file. The default value of
(π/180)2=0.0003046isused,iftheANGLEUNITkeywordisnotgivenintheforcefieldparameter
fileorthekeyfile.
ANGMAX [real] Set the maximum permissible angle between the current optimization search
direction and the negative of the gradient direction. If this maximum angle value is exceeded, the
optimization routine will note an error condition and may restart from the steepest descent
direction. The default value in the absence of the ANGMAX keyword is usually 88 degrees for
conjugategradientmethodsand180degrees(i.e.,disabled)forvariablemetricoptimizations.
ANISO-PRESSURE This keyword invokes use of full anisotropic pressure during dynamics
simulations. When using this option, the three axis lengths and axis angles vary separately in
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response to the pressure tensor. The default, in the absence of the keyword, is isotropic pressure
basedontheaverageofthediagonalofthepressuretensor.
ARCHIVEThiskeywordcausesTINKERmoleculardynamics-basedprogramstowritetrajectories
directlytoasingleplain-textarchivefilewiththe.arc format.Ifanarchivefilealreadyexistsatthe
startofthecalculation,thenthenewlygeneratedtrajectoryisappendedtotheendoftheexistingfile.
The default in the absence of this keyword is to write the trajectory snapshots to consecutively
numberedcyclefiles.
ATOM [2 integers, name, quoted string, integer, real & integer] This keyword provides the
valuesneededtodefineasingleforcefieldatomtype.
B-AXIS[real]Setsthevalueoftheb-axislengthforacrystalunitcell,or,equivalently,theY-axis
lengthforaperiodicbox.ThelengthvalueinAngstromsislistedafterthekeyword.Ifthekeywordis
absent,theb-axislengthissetequaltothea-axislength.
B-EXPTERM[real]Setsthevalueofthe``B''exponentialfactorintheBuckinghamvanderWaals
function,i.e.,thevalueofBintheformulaEvdw=ε{Aexp[-B(Ro/R)]-C(Ro/R)6}.
BAROSTAT [BERENDSEN] This keyword selects a barostat algorithm for use during molecular
dynamics.Atpresentonlyonemodifierisavailable,aBerendsenbathcouplingmethod.Thedefault
intheabsenceoftheBAROSTATkeywordistousetheBERENDSENalgorithm.
BASIN [2 reals] Presence of this keyword turns on a ``basin'' restraint potential function that
servestodrivethesystemtowardacompactstructure.TheactualfunctionisaGaussianoftheform
Ebasin=ΣAexp[-BR2],summedoverallpairsofatomswhereRisthedistancebetweenatoms.TheA
and B values are the depth and width parameters given as modifiers to the BASIN keyword. This
potential is currently used to control the degree of expansion during potential energy smooth
proceduresthroughtheuseofshallow,broadbasins.
BETA[real]Setsthevalueoftheβangleofacrystalunitcell,i.e.,theanglebetweenthea-axisand
c-axisofaunitcell,or,equivalently,theanglebetweentheX-axisandZ-axisofaperiodic box.The
defaultvalueintheabsenceoftheBETAkeywordistosettheβangleequaltotheαangleasgivenby
thekeywordALPHA.
BIOTYPE[integer,name,quotedstring&integer]Thiskeywordprovidesthevaluestodefine
thecorrespondencebetweenasinglebiopolymeratomtypeanditsforcefieldatomtype.
BOND [2 integers & 2 reals] This keyword provides the values for a single bond stretching
parameter.Theintegermodifiersgivetheatomclassnumbersforthetwokindsofatomsinvolvedin
thebondwhichistobedefined.Therealnumbermodifiersgivetheforceconstantvalueforthebond
andtheidealbondlengthin≈.Thedefaultunitsfortheforceconstantarekcal/mole/≈2,butthiscan
becontrolledviatheBONDUNITkeyword.
BOND-CUBIC [real] Sets the value of the cubic term in the Taylor series expansion form of the
bond stretching potential energy. The real number modifier gives the value of the coefficient as a
multiple of the quadratic coefficient. This term multiplied by the bond stretching energy unit
conversionfactor,theforceconstant,andthecubeofthedeviationofthebondlengthfromitsideal
valuegivesthecubiccontributiontothebondstretchingenergy.Thedefaultvalueintheabsenceof
theBOND-CUBICkeywordiszero;i.e.,thecubicbondstretchingtermisomitted.
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BOND-QUARTIC[real]SetsthevalueofthequartictermintheTaylorseriesexpansionformof
thebondstretchingpotentialenergy.Therealnumbermodifiergivesthevalueofthecoefficientasa
multiple of the quadratic coefficient. This term multiplied by the bond stretching energy unit
conversionfactor,theforceconstant,andtheforthpowerofthedeviationofthebondlengthfromits
ideal value gives the quartic contribution to the bond stretching energy. The default value in the
absenceoftheBOND-QUARTICkeywordiszero;i.e.,thequarticbondstretchingtermisomitted.
BOND3 [2 integers & 2 reals] This keyword provides the values for a single bond stretching
parameterspecifictoatomsin3-memberedrings.Theintegermodifiersgivetheatomclassnumbers
forthetwokindsofatomsinvolvedinthebondwhichistobedefined.Therealnumbermodifiers
give the force constant value for the bond and the ideal bond length in ≈. The default units for the
force constant are kcal/mole/≈2, but this can be controlled via the BONDUNIT keyword. If any
BOND3 keywords are present, either in the master force field parameter file or the keyfile, then
TINKERrequiresthatspecialBOND3parametersbegivenforallbondsin3-memberedrings.Inthe
absenceofanyBOND3keywords,standardBONDparameterswillbeusedforbondsin3-membered
rings.
BOND4 [2 integers & 2 reals] This keyword provides the values for a single bond stretching
parameterspecifictoatomsin4-memberedrings.Theintegermodifiersgivetheatomclassnumbers
forthetwokindsofatomsinvolvedinthebondwhichistobedefined.Therealnumbermodifiers
give the force constant value for the bond and the ideal bond length in ≈. The default units for the
force constant are kcal/mole/≈2, but this can be controlled via the BONDUNIT keyword. If any
BOND4 keywords are present, either in the master force field parameter file or the keyfile, then
TINKERrequiresthatspecialBOND4parametersbegivenforallbondsin4-memberedrings.Inthe
absenceofanyBOND4keywords,standardBONDparameterswillbeusedforbondsin4-membered
rings
BOND5 [2 integers & 2 reals] This keyword provides the values for a single bond stretching
parameterspecifictoatomsin5-memberedrings.Theintegermodifiersgivetheatomclassnumbers
forthetwokindsofatomsinvolvedinthebondwhichistobedefined.Therealnumbermodifiers
give the force constant value for the bond and the ideal bond length in ≈. The default units for the
force constant are kcal/mole/≈2, but this can be controlled via the BONDUNIT keyword. If any
BOND5 keywords are present, either in the master force field parameter file or the keyfile, then
TINKERrequiresthatspecialBOND5parametersbegivenforallbondsin5-memberedrings.Inthe
absenceofanyBOND5keywords,standardBONDparameterswillbeusedforbondsin5-membered
rings
BONDTERM [NONE/ONLY] This keyword controls use of the bond stretching potential energy
term. In the absence of a modifying option, this keyword turns on use of the potential. The NONE
option turns off use of this potential energy term. The ONLY option turns off all potential energy
termsexceptforthisone.
BONDTYPE [TAYLOR/MORSE/GAUSSIAN] Chooses the functional form of the bond stretching
potential. The TAYLOR option selects a Taylor series expansion containing terms from harmonic
through quartic. The MORSE option selects a Morse potential fit to the ideal bond length and
stretching force constant parameter values. The GAUSSIAN option uses an inverted Gaussian with
amplitude equal to the Morse bond dissociation energy and width set to reproduce the vibrational
frequencyofaharmonicpotential.ThedefaultistousetheTAYLORpotential.
BONDUNIT[real]Setsthescalefactorneededtoconverttheenergyvaluecomputedbythebond
stretchingpotentialintounitsofkcal/mole.Thecorrectvalueisforcefielddependentandtypically
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providedintheheaderofthemasterforcefieldparameterfile.Thedefaultvalueof1.0isused,ifthe
BONDUNITkeywordisnotgivenintheforcefieldparameterfileorthekeyfile.
C-AXIS[real]SetsthevalueoftheC-axislengthforacrystalunitcell,or,equivalently,theZ-axis
lengthforaperiodicbox.ThelengthvalueinAngstromsislistedafterthekeyword.Ifthekeywordis
absent,theC-axislengthissetequaltotheA-axislength.
C-EXPTERM [real] Sets the value of the ``C'' dispersion multiplier in the Buckingham van der
Waalsfunction,i.e.,thevalueofCintheformulaEvdw=ε{Aexp[-B(Ro/R)]-C(Ro/R)6}.
CAPPA [real] This keyword is used to set the normal termination criterion for the line search
phaseofTINKERoptimizationroutines.Thelinesearchexitssuccessfullyiftheratioofthecurrent
gradientprojectiononthelinetotheprojectionatthestartofthelinesearchfallsbelowthevalueof
CAPPA.Adefaultvalueof0.1isusedintheabsenceoftheCAPPAkeyword.
CHARGE [1 integer & 1 real] This keyword provides a value for a single atomic partial charge
electrostaticparameter.Theintegermodifier,ifpositive,givestheatomtypenumberforwhichthe
chargeparameteristobedefined.Notethatchargeparametersaregivenforatomtypes,notatom
classes. If the integer modifier is negative, then the parameter value to follow applies only to the
individualatomwhoseatomnumberisthenegativeofthemodifier.Therealnumbermodifiergives
thevaluesoftheatomicpartialchargeinelectrons.
CHARGETERM [NONE/ONLY] This keyword controls use of the charge-charge potential energy
term between pairs of atomic partial charges. In the absence of a modifying option, this keyword
turnsonuseofthepotential.TheNONEoptionturnsoffuseofthispotentialenergyterm.TheONLY
optionturnsoffallpotentialenergytermsexceptforthisone.
CHG-12-SCALE[real]Thiskeywordprovidesamultiplicativescalefactorthatisappliedtochargechargeelectrostaticinteractionsbetween1-2connectedatoms,i.e.,atomsthataredirectlybonded.
Thedefaultvalueof0.0isused,iftheCHG-12-SCALEkeywordisnotgivenineithertheparameter
fileorthekeyfile.
CHG-13-SCALE[real]Thiskeywordprovidesamultiplicativescalefactorthatisappliedtochargechargeelectrostaticinteractionsbetween1-3connectedatoms,i.e.,atomsseparatedbytwocovalent
bonds. The default value of 0.0 is used, if the CHG-13-SCALE keyword is not given in either the
parameterfileorthekeyfile.
CHG-14-SCALE[real]Thiskeywordprovidesamultiplicativescalefactorthatisappliedtochargecharge electrostatic interactions between 1-4 connected atoms, i.e., atoms separated by three
covalentbonds.Thedefaultvalueof1.0isused,iftheCHG-14-SCALEkeywordisnotgivenineither
theparameterfileorthekeyfile.
CHG-15-SCALE[real]Thiskeywordprovidesamultiplicativescalefactorthatisappliedtochargechargeelectrostaticinteractionsbetween1-5connectedatoms,i.e.,atomsseparatedbyfourcovalent
bonds. The default value of 1.0 is used, if the CHG-15-SCALE keyword is not given in either the
parameterfileorthekeyfile.
CHG-CUTOFF [real] Sets the cutoff distance value in Angstroms for charge-charge electrostatic
potentialenergyinteractions.Theenergyforanypairofsitesbeyondthecutoffdistancewillbesetto
zero.Otherkeywordscanbeusedtoselectasmoothingschemenearthecutoffdistance.Thedefault
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cutoff distance in the absence of the CHG-CUTOFF keyword is infinite for nonperiodic systems and
9.0forperiodicsystems.
CHG-TAPER [real] This keyword allows modification of the cutoff window for charge-charge
electrostatic potential energy interactions. It is similar in form and action to the TAPER keyword,
exceptthatitsvalueappliesonlytothecharge-chargepotential.Thedefaultvalueintheabsenceof
theCHG-TAPERkeywordistobeginthecutoffwindowat0.65ofthecorrespondingcutoffdistance.
CHGDPLTERM [NONE/ONLY] This keyword controls use of the charge-dipole potential energy
term between atomic partial charges and bond dipoles. In the absence of a modifying option, this
keywordturnsonuseofthepotential.TheNONEoptionturnsoffuseofthispotentialenergyterm.
TheONLYoptionturnsoffallpotentialenergytermsexceptforthisone.
COLLISION[real]SetsthevalueoftherandomcollisionfrequencyusedintheAndersenstochastic
collisiondynamicsthermostat.Thesuppliedvaluehasunitsoffs-1atom-1andismultipliedinternal
toTINKERbythetimestepinfsandN-2/3whereNisthenumberofatoms.Thedefaultvalueusedin
theabsenceoftheCOLLISIONkeywordis0.1whichisappropriateformanysystemsbutmayneed
adjustmenttoachieveadequatetemperaturecontrolwithoutperturbingthedynamics.
COMPRESS [real] Sets the value of the bulk solvent isothermal compressibility in Atm-1 for use
during pressure computation and scaling in molecular dynamics computations. The default value
usedintheabsenceoftheCOMPRESSkeywordis0.000046,appropriateforwater.Thisparameter
serves as a scale factor for the Groningen-style pressure bath coupling time, and its exact value
shouldnotbeofcriticalimportance.
CUTOFF[real]Setsthecutoffdistancevalueforallnonbondedpotentialenergyinteractions.The
energyforanyofthenonbondedpotentialsofapairofsitesbeyondthecutoffdistancewillbesetto
zero.Otherkeywordscanbeusedtoselectasmoothingschemenearthecutoffdistance,ortoapply
differentcutoffdistancestovariousnonbondedenergyterms.
DEBUGTurnsonprintingofdetailedinformationandintermediatevaluesthroughouttheprogress
of a TINKER computation; not recommended for use with large structures or full potential energy
functionssinceasummaryofeveryindividualinteractionwillusuallybeoutput.
DEFORM[real]Setstheamountofdiffusionequation-stylesmoothingthatwillbeappliedtothe
potentialenergysurfacewhenusingtheSMOOTHforcefield.Therealnumberoptionisequivalentto
the``time''valueintheoriginalPiela,etal.formalism;thelargerthevalue,thegreaterthesmoothing.
Thedefaultvalueiszero,meaningthatnosmoothingwillbeapplied.
DEGREES-FREEDOM[integer]Thiskeywordallowsmanualsettingofthenumberofdegreesof
freedomduringadynamicscalculation.Theintegermodifierisusedbythermostatingmethodsand
inotherplacesasthenumberofdegreesoffreedom,overridingthevaluedeterminedbytheTINKER
codeatdynamicsstartup.Intheabsenceofthekeyword,theprogramswillautomaticallycompute
the correct value based on the number of atoms active during dynamics, bond or other constrains,
anduseofperiodicboundaryconditions.
DELTA-HALGREN [real] Sets the value of the δ parameter in Halgren's buffered 14-7 vdw
potentialenergyfunctionalform.IntheabsenceoftheDELTA-HALGRENkeyword,adefaultvalueof
0.07isused.
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DIELECTRIC [real] Sets the value of the bulk dielectric constant used to damp all electrostatic
interactionenergiesforanyoftheTINKERelectrostaticpotentialfunctions.Thedefaultvalueisforce
fielddependent,butisusuallyequalto1.0(forAllinger'sMMforcefieldsthedefaultis1.5).
DIFFUSE-CHARGE[real]Thiskeywordisusedduringpotentialfunctionsmoothingproceduresto
specify the effective diffusion coefficient to be applied to the smoothed form of the Coulomb's Law
charge-chargepotentialfunction.IntheabsenceoftheDIFFUSE-CHARGEkeyword,adefaultvalueof
3.5isused.
DIFFUSE-TORSION[real]Thiskeywordisusedduringpotentialfunctionsmoothingprocedures
tospecifytheeffectivediffusioncoefficienttobeappliedtothesmoothedformofthetorsionangle
potential function. In the absence of the DIFFUSE-TORSION keyword, a default value of 0.0225 is
used.
DIFFUSE-VDW [real] This keyword is used during potential function smoothing procedures to
specify the effective diffusion coefficient to be applied to the smoothed Gaussian approximation to
theLennard-JonesvanderWaalspotentialfunction.IntheabsenceoftheDIFFUSE-VDWkeyword,a
defaultvalueof1.0isused.
DIGITS[integer]ThiskeywordcontrolsthenumberofdigitsofprecisionoutputbyTINKERin
reportingpotentialenergiesandatomiccoordinates.Theallowedvaluesfortheintegermodifierare
4, 6 and 8. Input values less than 4 will be set to 4, and those greater than 8 will be set to 8. Final
energyvaluesreportedbymostTINKERprogramswillcontainthespecifiednumberofdigitstothe
right of the decimal point. The number of decimal places to be output for atomic coordinates is
generallytwolargerthanthevalueofDIGITS.IntheabsenceoftheDIGITSkeywordadefaultvalueof
4isused,andenergieswillbereportedto4decimalplaceswithcoordinatesto6decimalplaces.
DIPOLE [2 integers & 2 reals] This keyword provides the values for a single bond dipole
electrostaticparameter.Theintegermodifiersgivetheatomtypenumbersforthetwokindsofatoms
involvedinthebonddipolewhichistobedefined.Therealnumbermodifiersgivethevalueofthe
bonddipoleinDebyesandthepositionofthedipolesitealongthebond.Ifthebonddipolevalueis
positive, then the first of the two atom types is the positive end of the dipole. For a negative bond
dipolevalue,thefirstatomtypelistedisnegative.Thepositionalongthebondisanoptionalmodifier
thatgivesthepostionofthedipolesiteasafractionbetweenthefirstatomtype(position=0)andthe
secondatomtype(position=1).Thedefaultforthedipolepositionintheabsenceofaspecifiedvalue
is0.5,placingthedipoleatthemidpointofthebond.
DIPOLE3 [2 integers & 2 reals] This keyword provides the values for a single bond dipole
electrostaticparameterspecifictoatomsin3-memberedrings.Theintegermodifiersgivetheatom
typenumbersforthetwokindsofatomsinvolvedinthebonddipolewhichistobedefined.Thereal
numbermodifiersgivethevalueofthebonddipoleinDebyesandthepositionofthedipolesitealong
the bond. The default for the dipole position in the absence of a specified value is 0.5, placing the
dipoleatthemidpointofthebond.IfanyDIPOLE3keywordsarepresent,eitherinthemasterforce
fieldparameterfileorthekeyfile,thenTINKERrequiresthatspecialDIPOLE3parametersbegiven
forallbonddipolesin3-memberedrings.IntheabsenceofanyDIPOLE3keywords,standardDIPOLE
parameterswillbeusedforbondsin3-memberedrings.
DIPOLE4 [2 integers & 2 reals] This keyword provides the values for a single bond dipole
electrostaticparameterspecifictoatomsin4-memberedrings.Theintegermodifiersgivetheatom
typenumbersforthetwokindsofatomsinvolvedinthebonddipolewhichistobedefined.Thereal
numbermodifiersgivethevalueofthebonddipoleinDebyesandthepositionofthedipolesitealong
the bond. The default for the dipole position in the absence of a specified value is 0.5, placing the
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dipoleatthemidpointofthebond.IfanyDIPOLE4keywordsarepresent,eitherinthemasterforce
fieldparameterfileorthekeyfile,thenTINKERrequiresthatspecialDIPOLE4parametersbegiven
forallbonddipolesin4-memberedrings.IntheabsenceofanyDIPOLE4keywords,standardDIPOLE
parameterswillbeusedforbondsin4-memberedrings.
DIPOLE5 [2 integers & 2 reals] This keyword provides the values for a single bond dipole
electrostaticparameterspecifictoatomsin5-memberedrings.Theintegermodifiersgivetheatom
typenumbersforthetwokindsofatomsinvolvedinthebonddipolewhichistobedefined.Thereal
numbermodifiersgivethevalueofthebonddipoleinDebyesandthepositionofthedipolesitealong
the bond. The default for the dipole position in the absence of a specified value is 0.5, placing the
dipoleatthemidpointofthebond.IfanyDIPOLE5keywordsarepresent,eitherinthemasterforce
fieldparameterfileorthekeyfile,thenTINKERrequiresthatspecialDIPOLE5parametersbegiven
forallbonddipolesin5-memberedrings.IntheabsenceofanyDIPOLE5keywords,standardDIPOLE
parameterswillbeusedforbondsin5-memberedrings.
DIPOLETERM [NONE/ONLY] This keyword controls use of the dipole-dipole potential energy
termbetweenpairsofbonddipoles.Intheabsenceofamodifyingoption,thiskeywordturnsonuse
ofthepotential.TheNONEoptionturnsoffuseofthispotentialenergyterm.TheONLYoptionturns
offallpotentialenergytermsexceptforthisone.
DIRECT-11-SCALE[real]Thiskeywordprovidesamultiplicativescalefactorthatisappliedtothe
permanent (direct) field due to atoms within a polarization group during an induced dipole
calculation, i.e., atoms that are in the same polarization group as the atom being polarized. The
defaultvalueof0.0isused,iftheDIRECT-11-SCALEkeywordisnotgivenineithertheparameterfile
orthekeyfile.
DIRECT-12-SCALE[real]Thiskeywordprovidesamultiplicativescalefactorthatisappliedtothe
permanent (direct) field due to atoms in 1-2 polarization groups during an induced dipole
calculation,i.e.,atomsthatareinpolarizationgroupsdirectlyconnectedtothegroupcontainingthe
atombeingpolarized.Thedefaultvalueof0.0isused,iftheDIRECT-12-SCALEkeywordisnotgiven
ineithertheparameterfileorthekeyfile.
DIRECT-13-SCALE[real]Thiskeywordprovidesamultiplicativescalefactorthatisappliedtothe
permanent (direct) field due to atoms in 1-3 polarization groups during an induced dipole
calculation, i.e., atoms that are in polarization groups separated by one group from the group
containing the atom being polarized. The default value of 0.0 is used, if the DIRECT-13-SCALE
keywordisnotgivenineithertheparameterfileorthekeyfile.
DIRECT-14-SCALE[real]Thiskeywordprovidesamultiplicativescalefactorthatisappliedtothe
permanent (direct) field due to atoms in 1-4 polarization groups during an induced dipole
calculation, i.e., atoms that are in polarization groups separated by two groups from the group
containing the atom being polarized. The default value of 1.0 is used, if the DIRECT-14-SCALE
keywordisnotgivenineithertheparameterfileorthekeyfile.
DIVERGE[real]ThiskeywordisusedbytheSADDLEprogramtosetthemaximumallowedvalue
oftheratioofthegradientlengthalongthepathtothetotalgradientnormattheendofacycleof
minimizationperpendiculartothepath.IfthevalueprovidedbytheDIVERGEkeywordisexceeded,
thenanothercycleofmaximizationalongthepathisrequired.Adefaultvalueof0.005isusedinthe
absenceoftheDIVERGEkeyword.
DPL-CUTOFF [real] Sets the cutoff distance value in Angstroms for bond dipole-bond dipole
electrostatic potential energy interactions. The energy for any pair of bond dipole sites beyond the
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cutoffdistancewillbesettozero.Otherkeywordscanbeusedtoselectasmoothingschemenearthe
cutoffdistance.ThedefaultcutoffdistanceintheabsenceoftheDPL-CUTOFFkeywordisessentially
infinitefornonperiodicsystemsand10.0forperiodicsystems.
DPL-TAPER[real]Thiskeywordallowsmodificationofthecutoffwindowsforbonddipole-bond
dipole electrostatic potential energy interactions. It is similar in form and action to the TAPER
keyword,exceptthatitsvalueappliesonlytothevdwpotential.Thedefaultvalueintheabsenceof
theDPL-TAPERkeywordistobeginthecutoffwindowat0.75ofthedipolecutoffdistance.
ECHO[textstring]Thepresenceofthiskeywordcauseswhatevertextfollowsitonthelinetobe
copied directly to the output file. This keyword is also active in parameter files. It has no default
value;ifnotextfollowstheECHOkeyword,ablanklineisplacedintheoutputfile.
ELECTNEG[3integers&1real]Thiskeywordprovidesthevaluesforasingleelectronegativity
bondlengthcorrectionparameter.Thefirsttwointegermodifiersgivetheatomclassnumbersofthe
atoms involved in the bond to be corrected. The third integer modifier is the atom class of an
electronegativeatom.Inthecaseofaprimarycorrection,anatomofthisthirdclassmustbedirectly
bondedtoanatomofthesecondatomclass.Forasecondarycorrection,thethirdclassisoneatom
removedfromanatomofthesecondclass.Therealnumbermodifieristhevaluein≈bywhichthe
originalidealbondlengthistobecorrected.
ENFORCE-CHIRALITYThiskeywordcausesthechiralityfoundatchiraltetravalentcentersinthe
inputstructuretobemaintainedduringTINKERcalculations.Thetestforchiralityisnotexhaustive;
twoidenticalmonovalentatomsconnectedtoacentercauseittobemarkedasnon-chiral,butlarge
equivalentsubstituentsarenotdetected.Trivalent``chiral''centers,forexamplethealphacarbonin
united-atomproteinstructures,arenotenforcedaschiral.
EPSILONRULE [GEOMETRIC/ARITHMETIC/HARMONIC/HHG] This keyword selects the
combiningruleusedtoderivetheεvalueforvanderWaalsinteractions.Thedefaultintheabsence
oftheEPSILONRULEkeywordistousetheGEOMETRICmeanoftheindividualεvaluesofthetwo
atomsinvolvedinthevanderWaalsinteraction.
EWALDThiskeywordturnsontheuseofEwaldsummationduringcomputationofelectrostatic
interactions in periodic systems. In the current version of TINKER, regular Ewald is used for
polarizable atomic multipoles, and smooth particle mesh Ewald (PME) is used for charge-charge
interactions.Ewaldsummationisnotavailableforinteractionsinvolvingbond-centereddipoles.By
default, in the absence of the EWALD keyword, distance-based cutoffs are used for electrostatic
interactions.
EWALD-ALPHA [real] Sets the value of the Ewald coefficient which controls the width of the
Gaussian screening charges during particle mesh Ewald summation. In the absence of the EWALDALPHA keyword, a value is chosen which causes interactions outside the real-space cutoff to be
below a fixed tolerance. For most standard applications of Ewald summation, the program default
shouldbeused.
EWALD-BOUNDARYThiskeywordinvokestheuseofinsulating(ie,vacuum)boundaryconditions
during Ewald summation, corresponding to the media surrounding the system having a dielectric
value of 1. The default in the absence of the EWALD-BOUNDARY keyword is to use conducting (ie,
tinfoil)boundaryconditionswherethesurroundingmediaisassumedtohaveaninfinitedielectric
value.
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EWALD-CUTOFF[real]SetsthevalueinAngstromsofthereal-spacedistancecutoffforuseduring
Ewaldsummation.Bydefault,intheabsenceoftheEWALD-CUTOFFkeyword,avalueof9.0isused.
EXIT-PAUSEThiskeywordcausesTINKERprogramstopauseandwaitforacarriagereturnatthe
end of executation prior to returning control to the operating system. This is useful to keep the
execution window open following termination on machines running Microsoft Windows or Apple
MacOS.ThedefaultintheabsenceoftheEXIT-PAUSEkeyword,istoreturncontroltotheoperating
systemimmediatelyatprogramtermination.
EXTRATERM[NONE/ONLY]Thiskeywordcontrolsuseoftheuserdefinedextrapotentialenergy
term. In the absence of a modifying option, this keyword turns on use of the potential. The NONE
option turns off use of this potential energy term. The ONLY option turns off all potential energy
termsexceptforthisone.
FCTMIN[real]ThiskeywordsetsaconvergencecriterionforsuccessfulcompletionofaTINKER
optimization. If the value of the optimization objective function, typically the potential energy, falls
below the value set by FCTMIN, then the optimization is deemed to have converged. The default
value in the absence of the FCTMIN keyword is -1000000, effectively removing this criterion as a
possibleagentfortermination.
FORCEFIELD[name]Thiskeywordprovidesanamefortheforcefieldtobeusedinthecurrent
calculation.Itsvalueisusuallysetinthemasterforcefieldparameterfileforthecalculation(seethe
PARAMETERSkeyword)insteadofinthekeyfile.
FRICTION[real]Setsthevalueofthefrictionalcoefficientinps-1forusewithstochasticdynamics.
The default value used in the absence of the FRICTION keyword is 91.0, which is generally
appropriateforwater.
FRICTION-SCALING This keyword turns on the use of atomic surface area-based scaling of the
frictional coefficient during stochastic dynamics. When in use, the coefficient for each atom is
multipliedbythatatom'sfractionofexposedsurfacearea.Thedefaultintheabsenceofthekeyword
istoomitthescalingandusethefullcoefficientvalueforeachatom.
GAMMA[real]Setsthevalueoftheγangleofacrystalunitcell,i.e.,theanglebetweenthea-axis
andb-axisofaunitcell,or,equivalently,theanglebetweentheX-axisandY-axisofaperiodicbox.
ThedefaultvalueintheabsenceoftheGAMMAkeywordistosettheγangleequaltotheαangleas
givenbythekeywordALPHA.
GAMMA-HALGREN [real] Sets the value of the γ parameter in Halgren's buffered 14-7 vdw
potentialenergyfunctionalform.IntheabsenceoftheDELTA-HALGRENkeyword,adefaultvalueof
0.12isused.
GAMMAMIN[real]Setstheconvergencetargetvalueforγduringsearchesformaximaalongthe
quadraticsynchronoustransitusedbytheSADDLEprogram.Thevalueofγisthesquareoftheratio
ofthegradientprojectionalongthepathtothetotalgradient.Adefaultvalueof0.00001isusedin
theabsenceoftheGAMMAMINkeyword.
GAUSSTYPE[LJ-2/LJ-4/MM2-2/MM3-2/IN-PLACE]Thiskeywordspecifiestheunderlyingvdw
formthataGaussianvdwapproximationwillattempttofit.numberoftermstobeusedinaGaussian
approximationoftheLennard-JonesvanderWaalspotential.Thetextmodifiergivesthenameofthe
functionalformtobeused.ThusLJ-2asamodifierwillresultina2-GaussianfittoaLennard-Jones
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vdwpotential.TheGAUSSTYPEkeywordonlytakeseffectwhenVDWTYPEissettoGAUSSIAN.This
keywordhasnodefaultvalue.
GROUP[integer,integerlist]Thiskeyworddefinesanatomgroupasasubstructurewithinthe
fullinputmolecularstructure.Thevalueofthefirstintegeristhegroupnumberwhichmustbeinthe
rangefrom1tothemaximumnumberofallowedgroups.Theremainingintergersgivetheatomor
atomscontainedinthisgroupasoneormoreatomnumbersorranges.Multiplekeywordlinescan
beusedtospecifyadditionalatomsinthesamegroup.Notethatanatomcanonlybeinonegroup,
thelastgrouptowhichitisassignedistheoneused.
GROUP-INTERThiskeywordassignsavalueof1.0toallinter-groupinteractionsandavalueof0.0
to all intra-group interactions. For example, combination with the GROUP-MOLECULE keyword
providesforrigid-bodycalculations.
GROUP-INTRAThiskeywordassignsavalueof1.0toallintra-groupinteractionsandavalueof
0.0toallinter-groupinteractions.
GROUP-MOLECULE This keyword sets each individual molecule in the system to be a separate
atomgroup,butdoesnotassignweightstogroup-groupinteractions.
GROUP-SELECT[2integers,real]Thiskeywordgivestheweightinthefinalpotentialenergyofa
specifiedsetofintra-orintergroupinteractions.Theintegermodifiersgivethegroupnumbersofthe
groupsinvolved.Ifthetwonumbersarethesame,thenanintragroupsetofinteractionsisspecified.
The real modifier gives the weight by which all energetic interactions in this set will be multiplied
beforeincorporationintothefinalpotentialenergy.Ifomittedasakeywordmodifier,theweightwill
besetto1.0bydefault.IfanySELECT-GROUPkeywordsarepresent,thenanysetofinteractionsnot
specifiedinaSELECT-GROUPkeywordisgivenazeroweight.ThedefaultwhennoSELECT-GROUP
keywords are specified is to use all intergroup interactions with a weight of 1.0 and to set all
intragroupinteractionstozero.
HBOND [2 integers & 2 reals] This keyword provides the values for the MM3-style directional
hydrogenbondingparametersforasinglepairofatoms.Theintegermodifiersgivethepairofatom
class numbers for which hydrogen bonding parameters are to be defined. The two real number
modifiers give the values of the minimum energy contact distance in ≈ and the well depth at the
minimumdistanceinkcal/mole.
HESS-CUTOFF[real]ThiskeyworddefinesalowerlimitforsignificantHessianmatrixelements.
During computation of the Hessian matrix of partial second derivatives, any matrix elements with
absolutevaluebelowHESS-CUTOFFwillbesettozeroandomittedfromthesparsematrixHessian
storageschemeusedbyTINKER.Formostcalculations,thedefaultintheabsenceofthiskeywordis
zero, i.e., all elements will be stored. For most Truncated Newton optimizations the Hessian cutoff
willbechosendynamicallybytheoptimizer.
HGUESS [real] Sets an initial guess for the average value of the diagonal elements of the scaled
inverse Hessian matrix used by the optimally conditioned variable metric optimization routine. A
defaultvalueof0.4isusedintheabsenceoftheHGUESSkeyword.
IMPROPER[4integers&2reals]ThiskeywordprovidesthevaluesforasingleCHARMM-style
improperdihedralangleparameter.
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IMPROPTERM[NONE/ONLY]ThiskeywordcontrolsuseoftheCHARMM-styleimproperdihedral
anglepotentialenergyterm.Intheabsenceofamodifyingoption,thiskeywordturnsonuseofthe
potential.TheNONEoptionturnsoffuseofthispotentialenergyterm.TheONLYoptionturnsoffall
potentialenergytermsexceptforthisone.
IMPROPUNIT [real] Sets the scale factor needed to convert the energy value computed by the
CHARMM-styleimproperdihedralanglepotentialintounitsofkcal/mole.Thecorrectvalueisforce
field dependent and typically provided in the header of the master force field parameter file. The
defaultvalueof1.0isused,iftheIMPROPUNITkeywordisnotgivenintheforcefieldparameterfile
orthekeyfile.
IMPTORS[4integers&upto3real/real/integertriples]Thiskeywordprovidesthevaluesfor
a single AMBER-style improper torsional angle parameter. The first four integer modifiers give the
atom class numbers for the atoms involved in the improper torsional angle to be defined. By
convention, the third atom class of the four is the trigonal atom on which the improper torsion is
centered.Thetorsionalanglecomputedisliterallythatdefinedbythefouratomclassesintheorder
specifiedbythekeyword.Eachoftheremainingtriplesofreal/real/integermodifiersgivethehalfamplitude, phase offset in degrees and periodicity of a particular improper torsional term,
respectively.Periodicitiesthrough3-foldareallowedforimpropertorsionalparameters.
IMPTORSTERM[NONE/ONLY]ThiskeywordcontrolsuseoftheAMBER-styleimpropertorsional
anglepotentialenergyterm.Intheabsenceofamodifyingoption,thiskeywordturnsonuseofthe
potential.TheNONEoptionturnsoffuseofthispotentialenergyterm.TheONLYoptionturnsoffall
potentialenergytermsexceptforthisone.
IMPTORSUNIT[real]Setsthescalefactorneededtoconverttheenergyvaluecomputedbythe
AMBER-style improper torsional angle potential into units of kcal/mole. The correct value is force
field dependent and typically provided in the header of the master force field parameter file. The
defaultvalueof1.0isused,iftheIMPTORSUNITkeywordisnotgivenintheforcefieldparameterfile
orthekeyfile.
INACTIVE[integerlist]SetsthelistofinactiveatomsduringaTINKERcomputation.Individual
potential energy terms are not computed when all atoms involved in the term are inactive. For
Cartesian space calculations, inactive atoms are not allowed to move. For torsional space
calculations, rotations are not allowed when there are inactive atoms on both sides of the rotated
bond. Multiple INACTIVE lines can be present in the keyfile, and on each line the keyword can be
followedbyoneormoreatomnumbersorranges.IfanyINACTIVEkeysarefound,allatomsareset
to active except those listed on the INACTIVE lines. The ACTIVE keyword overrides all INACTIVE
keywordsfoundinthekeyfile.
INTEGRATE[VERLET/BEEMAN/STOCHASTIC/RIGIDBODY]Choosestheintegrationmethodfor
propagationofdynamicstrajectories.Thekeywordisfollowedonthesamelinebythenameofthe
option.StandardNewtonianMDcanberunusingeitherVERLETfortheVelocityVerletmethod,or
BEEMAN for the velocity form of Bernie Brook's ``Better Beeman'' method. A Velocity Verlet-based
stochastic dynamics trajectory is selected by the STOCHASTIC modifier. A rigid-body dynamics
method is selected by the RIGIDBODY modifier. The default integration scheme is MD using the
BEEMANmethod.
INTMAX[integer]Setsthemaximumnumberofinterpolationcyclesthatwillbeallowedduring
the line search phase of an optimization. All gradient-based TINKER optimization routines use a
commonlinesearchroutineinvolvingquadraticextrapolationandcubicinterpolation.Ifthevalueof
INTMAXisreached,anerrorstatusissetforthelinesearchandthesearchisrepeatedwithamuch
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smaller initial step size. The default value in the absence of this keyword is optimization routine
dependent,butisusuallyintherange5to10.
LAMBDA[real]Thiskeywordsetsthevalueoftheλpathparameterforfreeenergyperturbation
calculations.Therealnumbermodifierspecifiesthepositionalongthemutationpathandmustbea
numberintherangefrom0(initialstate)to1(finalstate).Theactualatomsinvolvedinthemutation
aregivenseparatelyinindividualMUTATEkeywordlines.
LBFGS-VECTORS[integer]Setsthenumberofcorrectionvectorsusedbythelimited-memoryLBFGSoptimizationroutine.Thecurrentmaximumallowablevalue,andthedefaultintheabsenceof
theLBFGS-VECTORSkeywordis15.
LIGHTS This keyword turns on Method of Lights neighbor generation for the partial charge
electrostatics and any of the van der Waals potentials. This method will yield identical energetic
results to the standard double loop method. Method of Lights will be faster when the volume of a
spherewithradiusequaltothenonbondcutoffdistanceissignificantlylessthanhalfthevolumeof
thetotalsystem(i.e.,thefullmolecularsystem,thecrystalunitcellortheperiodicbox).Itrequires
lessstoragethanpairwiseneighborlists.
LIST-BUFFER[real]SetsthesizeoftheneighborlistbufferinAngstroms.Thisvalueisaddedto
theactualcutoffdistancetodeterminewhichpairswillbekeptontheneighborlist.Thesamebuffer
valueisusedforallneighborlists.Thedefaultvalueintheabsenceof2.0isusedintheabsenceofthe
LIST-BUFFERkeyword.
MAXITER[integer]Setsthemaximumnumberofminimizationiterationsthatwillbeallowedfor
anyTINKERprogramthatusesanyofthenonlinearoptimizationroutines.Thedefaultvalueinthe
absenceofthiskeywordisprogramdependent,butisalwayssettoaverylargenumber.
METALThiskeywordprovidesthevaluesforasingletransitionmetalligandfieldparameter.Note
thiskeywordispresentinthecode,butnotactiveinthecurrentversionofTINKER.
METALTERM [NONE/ONLY] This keyword controls use of the transition metal ligand field
potential energy term. In the absence of a modifying option, this keyword turns on use of the
potential.TheNONEoptionturnsoffuseofthispotentialenergyterm.TheONLYoptionturnsoffall
potentialenergytermsexceptforthisone.
MM2-STRBNDThiskeywordswitchesthebehaviorofthestretch-bendpotentialfunctiontomatch
the formulation used by the MM2 force field. In MM2, stretching of bonds to attached hydrogen
atomsisnotincludingincomputingthestretch-bendcrosstermenergy.Thedefaultbehaviorinthe
absence of this keyword is to include stretching of attached hydrogen atoms as in the MM3 force
field.
MPOLE-12-SCALE [real] This keyword provides a multiplicative scale factor that is applied to
permanentatomicmultipoleelectrostaticinteractionsbetween1-2connectedatoms,i.e.,atomsthat
aredirectlybonded.Thedefaultvalueof0.0isused,iftheMPOLE-12-SCALEkeywordisnotgivenin
eithertheparameterfileorthekeyfile.
MPOLE-13-SCALE [real] This keyword provides a multiplicative scale factor that is applied to
permanent atomic multipole electrostatic interactions between 1-3 connected atoms, i.e., atoms
separatedbytwocovalentbonds.Thedefaultvalueof0.0isused,iftheMPOLE-13-SCALEkeywordis
notgivenineithertheparameterfileorthekeyfile.
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MPOLE-14-SCALE [real] This keyword provides a multiplicative scale factor that is applied to
permanent atomic multipole electrostatic interactions between 1-4 connected atoms, i.e., atoms
separatedbythreecovalentbonds.Thedefaultvalueof1.0isused,iftheMPOLE-14-SCALEkeyword
isnotgivenineithertheparameterfileorthekeyfile.
MPOLE-15-SCALE [real] This keyword provides a multiplicative scale factor that is applied to
permanent atomic multipole electrostatic interactions between 1-5 connected atoms, i.e., atoms
separatedbyfourcovalentbonds.Thedefaultvalueof1.0isused,iftheMPOLE-15-SCALEkeyword
isnotgivenineithertheparameterfileorthekeyfile.
MPOLE-CUTOFF[real]SetsthecutoffdistancevalueinAngstromsforatomicmultipolepotential
energy interactions. The energy for any pair of sites beyond the cutoff distance will be set to zero.
Otherkeywordscanbeusedtoselectasmoothingschemenearthecutoffdistance.Thedefaultcutoff
distanceintheabsenceoftheMPOLE-CUTOFFkeywordisinfinitefornonperiodicsystemsand9.0
forperiodicsystems.
MPOLE-TAPER[real]Thiskeywordallowsmodificationofthecutoffwindowforatomicmultipole
potentialenergyinteractions.ItissimilarinformandactiontotheTAPERkeyword,exceptthatits
valueappliesonlytotheatomicmultipolepotential.ThedefaultvalueintheabsenceoftheMPOLETAPERkeywordistobeginthecutoffwindowat0.65ofthecorrespondingcutoffdistance.
MPOLETERM [NONE/ONLY] This keyword controls use of the atomic multipole electrostatics
potential energy term. In the absence of a modifying option, this keyword turns on use of the
potential.TheNONEoptionturnsoffuseofthispotentialenergyterm.TheONLYoptionturnsoffall
potentialenergytermsexceptforthisone.
MULTIPOLE [5 lines with: 3 or 4 integers & 1 real; 3 reals; 1 real; 2 reals; 3 reals] This
keyword provides the values for a set of atomic multipole parameters at a single site. A complete
keywordentryconsistsofthreeconsequtivelines,thefirstlinecontainingtheMULTIPOLEkeyword
and the two following lines. The first line contains three integers which define the atom type on
whichthemultipolesarecentered,andtheZ-axisandX-axisdefiningatomtypesforthiscenter.The
optionalfourthintegercontainstheY-axisdefiningatomtype,andisonlyrequiredforlocallychiral
multipole sites. The real number on the first line gives the monopole (atomic charge) in electrons.
ThesecondlinecontainsthreerealnumberswhichgivetheX-,Y-andZ-componentsoftheatomic
dipole in electron-≈. The final three lines, consisting of one, two and three real numbers give the
uppertriangleofthetracelessatomicquadrupoletensorinelectron-≈2.
MUTATE [3 integers] This keyword is used to specify atoms to be mutated during free energy
perturbationcalculations.Thefirstintegermodifiergivestheatomnumberofanatominthecurrent
system.Thefinaltwomodifiervaluesgivetheatomtypescorrespondingthetheλ=0andλ=1states
ofthespecifiedatom.
MUTUAL-11-SCALE[real]Thiskeywordprovidesamultiplicativescalefactorthatisappliedto
the induced (mutual) field due to atoms within a polarization group during an induced dipole
calculation, i.e., atoms that are in the same polarization group as the atom being polarized. The
defaultvalueof1.0isused,iftheMUTUAL-11-SCALEkeywordisnotgivenineithertheparameter
fileorthekeyfile.
MUTUAL-12-SCALE[real]Thiskeywordprovidesamultiplicativescalefactorthatisappliedto
the induced (mutual) field due to atoms in 1-2 polarization groups during an induced dipole
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calculation,i.e.,atomsthatareinpolarizationgroupsdirectlyconnectedtothegroupcontainingthe
atombeingpolarized.Thedefaultvalueof1.0isused,iftheMUTUAL-12-SCALEkeywordisnotgiven
ineithertheparameterfileorthekeyfile.
MUTUAL-13-SCALE[real]Thiskeywordprovidesamultiplicativescalefactorthatisappliedto
the induced (mutual) field due to atoms in 1-3 polarization groups during an induced dipole
calculation, i.e., atoms that are in polarization groups separated by one group from the group
containing the atom being polarized. The default value of 1.0 is used, if the MUTUAL-13-SCALE
keywordisnotgivenineithertheparameterfileorthekeyfile.
MUTUAL-14-SCALE[real]Thiskeywordprovidesamultiplicativescalefactorthatisappliedto
the induced (mutual) field due to atoms in 1-4 polarization groups during an induced dipole
calculation, i.e., atoms that are in polarization groups separated by two groups from the group
containing the atom being polarized. The default value of 1.0 is used, if the MUTUAL-14-SCALE
keywordisnotgivenineithertheparameterfileorthekeyfile.
NEIGHBOR-GROUPS This keyword causes the attached atom to be used in determining the
charge-chargeneighbordistanceforallmonovalentatomsinthemolecularsystem.Itsusecausesall
monovalentatomstobetreatedthesameastheirattachedatomsforpurposesofincludingorscaling
1-2, 1-3 and 1-4 interactions. This option works only for the simple charge-charge electrostatic
potential; it does not affect bond dipole or atomic multipole potentials. The NEIGHBOR-GROUPS
schemeissimilartothatusedbysomecommonforcefieldssuchasENCAD.
NEIGHBOR-LISTThiskeywordturnsonpairwiseneighborlistsforpartialchargeelectrostatics,
polarize multipole electrostatics and any of the van der Waals potentials. This method will yield
identicalenergeticresultstothestandarddoubleloopmethod.
NEUTRAL-GROUPSThiskeywordcausestheattachedatomtobeusedindeterminingthechargechargeinteractioncutoffdistanceforallmonovalentatomsinthemolecularsystem.Itsusereduces
cutoff discontinuities by avoiding splitting many of the largest charge separations found in typical
molecules. Note that this keyword does not rigorously implement the usual concept of a ``neutral
group''asusedintheliteraturewithAMBER/OPLSandotherforcefields.Thisoptionworksonlyfor
the simple charge-charge electrostatic potential; it does not affect bond dipole or atomic multipole
potentials.
NEWHESS [integer] Sets the number of algorithmic iterations between recomputation of the
Hessian matrix. At present this keyword applies exclusively to optimizations using the Truncated
Newtonmethod.Thedefaultvalueintheabsenceofthiskeywordis1,i.e.,theHessianiscomputed
oneveryiteration.
NEXTITER [integer] Sets the iteration number to be used for the first iteration of the current
computation. At present this keyword applies to optimization procedures where its use can effect
convergencecriteria,timingofrestarts,andsoforth.Thedefaultintheabsenceofthiskeywordisto
taketheinitialiterationasiteration1.
NOSE-MASS[real]ThiskeywordsetsthemassofparticlesmakinguptheNose-Hooverchainin
thatthermostatingmethod.ThedefaultintheabsenceoftheNOSE-MASSkeywordistouseamassof
0.1.
NOVERSIONTurnsofftheuseofversionnumbersappendedtotheendoffilenamesasthemethod
forgeneratingfilenamesforupdatedcopiesofanexistingfile.Thepresenceofthiskeywordresults
indirectuseofinputfilenameswithoutasearchforthehighestavailableversion,andrequiresthe
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entry of specific output file names in many additional cases. By default, in the absence of this
keyword, TINKER generates and attaches version numbers in a manner similar to the Digital
OpenVMS operating system. For example, subsequent new versions of the file molecule.xyz
wouldbewrittenfirsttothefile molecule.xyz_2,thentomolecule.xyz_3,etc.
OCTAHEDRONSpecifiesthattheperiodic``box''isatruncatedoctahedronwithmaximaldistance
acrossthetruncatedoctahedronasgivenbytheA-AXISkeyword.Allotherunitcellandperiodicbox
size-definingkeywordsareignorediftheOCTAHEDRONkeywordispresent.
OPBEND[2integers&1real]ThiskeywordprovidesthevaluesforasingleAllingerMM-style
out-of-plane angle bending potential parameter. The first integer modifier is the atom class of the
central trigonal atom and the second integer is the atom class of the out-of-plane atom. The real
numbermodifiergivestheforceconstantvaluefortheout-of-planeangle.Thedefaultunitsforthe
forceconstantarekcal/mole/radian2,butthiscanbecontrolledviatheOPBENDUNITkeyword.
OPBENDTERM [NONE/ONLY] This keyword controls use of the Allinger MM-style out-of-plane
bendingpotentialenergyterm.Intheabsenceofamodifyingoption,thiskeywordturnsonuseofthe
potential.TheNONEoptionturnsoffuseofthispotentialenergyterm.TheONLYoptionturnsoffall
potentialenergytermsexceptforthisone.
OPBENDUNIT [real] Sets the scale factor needed to convert the energy value computed by the
AllingerMM-styleout-of-planebendingpotentialintounitsofkcal/mole.Thecorrectvalueisforce
field dependent and typically provided in the header of the master force field parameter file. The
defaultof(π/180)2=0.0003046isused,iftheOPBENDUNITkeywordisnotgivenintheforcefield
parameterfileorthekeyfile.
OPDIST[4integers&1real]Thiskeywordprovidesthevaluesforasingleout-of-planedistance
potentialparameter.Thefirstintegermodifieristheatomclassofthecentraltrigonalatomandthe
threefollowingintegermodifiersaretheatomclassesofthethreeattachedatoms.Therealnumber
modifier is the force constant for the harmonic function of the out-of-plane distance of the central
atom. The default units for the force constant are kcal/mole/≈2, but this can be controlled via the
OPDISTUNITkeyword.
OPDISTTERM [NONE/ONLY] This keyword controls use of the out-of-plane distance potential
energy term. In the absence of a modifying option, this keyword turns on use of the potential. The
NONE option turns off use of this potential energy term. The ONLY option turns off all potential
energytermsexceptforthisone.
OPDISTUNIT[real]Setsthescalefactorneededtoconverttheenergyvaluecomputedbytheoutof-plane distance potential into units of kcal/mole. The correct value is force field dependent and
typically provided in the header of the master force field parameter file. The default value of 1.0 is
used,iftheOPDISTUNITkeywordisnotgivenintheforcefieldparameterfileorthekeyfile.
OVERWRITE Causes TINKER programs, such as minimizations, that output intermediate
coordinate sets to create a single disk file for the intermediate results which is successively
overwritten with the new intermediate coordinates as they become available. This keyword is
essentiallytheoppositeoftheSAVECYCLEkeyword.
PARAMETERS[filename]Providesthenameoftheforcefieldparameterfiletobeusedforthe
current TINKER calculation. The standard file name extension for parameter files, .prm, is an
optionalpartofthefilenamemodifier.ThedefaultintheabsenceofthePARAMETERSkeywordisto
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lookforaparameterfilewiththesamebasenameasthemolecularsystemandendinginthe.prm
extension. If a valid parameter file is not found, the user will asked to provide a file name
interactively.
PIATOM[1integer&3reals]ThiskeywordprovidesthevaluesforthepisystemMOpotential
parametersforasingleatomclassbelongingtoapisystem.
PIBOND[2integers&2reals]ThiskeywordprovidesthevaluesforthepisystemMOpotential
parametersforasingletypeofpisystembond.
PIBOND4[2integers&2reals]ThiskeywordprovidesthevaluesforthepisystemMOpotential
parametersforasingletypeofpisystembondcontainedina4-memberedring.
PIBOND5[2integers&2reals]ThiskeywordprovidesthevaluesforthepisystemMOpotential
parametersforasingletypeofpisystembondcontainedina5-memberedring.
PISYSTEM [integer list] This keyword sets the atoms within a molecule that are part of a
conjugated π-system. The keyword is followed on the same line by a list of atom numbers and/or
atomrangesthatconstitutetheπ-system.TheAllingerMMforcefieldsusethisinformationtosetup
anMOcalculationusedtoscalebondandtorsionparametersinvolvingπ-systematoms.
PITORS[2integers&1real]Thiskeywordprovidesthevaluesforasinglepi-orbitaltorsional
angle potential parameter. The two integer modifiers give the atom class numbers for the atoms
involvedinthecentralbondofthetorsionalangletobeparameterized.Therealmodifiergivesthe
value of the 2-fold Fourier amplitude for the torsional angle between p-orbitals centered on the
definedbondatomclasses.Thedefaultunitsforthestretch-torsionforceconstantcanbecontrolled
viathePITORSUNITkeyword.
PITORSTERM[NONE/ONLY]Thiskeywordcontrolsuseofthepi-orbitaltorsionalanglepotential
energy term. In the absence of a modifying option, this keyword turns on use of the potential. The
NONE option turns off use of this potential energy term. The ONLY option turns off all potential
energytermsexceptforthisone.
PITORSUNIT[real]Setsthescalefactorneededtoconverttheenergyvaluecomputedbythepiorbital torsional angle potential into units of kcal/mole. The correct value is force field dependent
andtypicallyprovidedintheheaderofthemasterforcefieldparameterfile.Thedefaultvalueof1.0
isused,ifthePITORSUNITkeywordisnotgivenintheforcefieldparameterfileorthekeyfile.
PME-GRID[3integers]Thiskeywordsetsthedimensionsofthechargegridusedduringparticle
meshEwaldsummation.ThethreemodifiersgivethesizealongtheX-,Y-andZ-axes,respectively.If
eithertheY-orZ-axisdimensionsareomitted,thentheyaresetequaltotheX-axisdimension.The
defaultintheabsenceofthePME-GRIDkeywordistosetthegridsizealongeachaxistothesmallest
powerof2,3and/or5whichisatleastaslargeas1.5timestheaxislengthinAngstoms.Notethat
theFFTusedbyPMEisnotrestrictedto,butismostefficientfor,gridsizeswhicharepowersof2,3
and/or5.
PME-ORDER [integer] This keyword sets the order of the B-spline interpolation used during
particle mesh Ewald summation. A default value of 8 is used in the absence of the PME-ORDER
keyword.
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POLAR-12-SCALE [real] This keyword provides a multiplicative scale factor that is applied to
polarization interactions between 1-2 polarization groups, i.e., pairs of atoms that are in directly
connectedpolarizationgroups.Thedefaultvalueof0.0isused,ifthePOLAR-12-SCALEkeywordis
notgivenineithertheparameterfileorthekeyfile.
POLAR-13-SCALE [real] This keyword provides a multiplicative scale factor that is applied to
polarizationinteractionsbetween1-3polarizationgroups,i.e.,pairsofatomsthatareinpolarization
groups separated by one other group. The default value of 0.0 is used, if the POLAR-13-SCALE
keywordisnotgivenineithertheparameterfileorthekeyfile.
POLAR-14-SCALE [real] This keyword provides a multiplicative scale factor that is applied to
polarizationinteractionsbetween1-4polarizationgroups,i.e.,pairsofatomsthatareinpolarization
groups separated by two other groups. The default value of 1.0 is used, if the POLAR-14-SCALE
keywordisnotgivenineithertheparameterfileorthekeyfile.
POLAR-15-SCALE [real] This keyword provides a multiplicative scale factor that is applied to
polarizationinteractionsbetween1-5polarizationgroups,i.e.,pairsofatomsthatareinpolarization
groups separated by three other groups. The default value of 1.0 is used, if the POLAR-15-SCALE
keywordisnotgivenineithertheparameterfileorthekeyfile.
POLAR-DAMP[2reals]Controlsthestrengthofthedampingfunctionappliedtoinduceddipoles
and dipole polarization interaction energies. The first modifier sets the radius in Angstoms of a
hypothetical atom with unit polarizability, while the second modifier sets the scale factor for the
exponentofthedampingfunction.Thedefaultvaluesfortheradiusandthescalefactorare1.662
and1.0,respectively.Dampingiseliminatedentirelybyusingthiskeywordtosettheradiusvalueto
zero.
POLAR-EPS [real] This keyword sets the convergence criterion applied during computation of
self-consistent induced dipoles. The calculation is deemed to have converged when therms change
(in Debyes) of the induced dipoles at all polarizable sites is less than the value specified with this
keyword.Thedefaultvalueintheabsenceofthekeywordis10-6Debyes.
POLAR-SOR[real]Setsasuccessiveoverrelaxation(SOR)factorforuseincomputationofinduced
atomicdipoles.Optimalvaluesforthiskeywordwillspeedtheinduceddipolecalculation,andpoor
valuescanresultinconvergencefailure.ThedefaultvalueintheabsenceofthePOLAR-SORkeyword
is 0.7 which often a reasonable value when short-range intramolecular polarization is present. For
modelslackingintramolecularpolarization,keywordvaluescloserto1.0maybeoptimal.
POLARIZATION [DIRECT/MUTUAL] Selects between the use of direct and mutual dipole
polarization for force fields that incorporate the polarization term. The DIRECT modifier avoids an
iterative calculation by using only the permanent electric field in computation of induced dipoles.
TheMUTUALoption,whichisthedefaultintheabsenceofthePOLARIZATIONkeyword,iteratesthe
induceddipolestoself-consistency.
POLARIZE[1integer,1real&upto4integers]Thiskeywordprovidesthevaluesforasingle
atomicdipolepolarizabilityparameter.Theintegermodifier,ifpositive,givestheatomtypenumber
forwhichapolarizabilityparameteristobedefined.Ifthefirstintegermodifierisnegative,thenthe
parametervaluetofollowappliesonlytotheindividualatomwhoseatomnumberisthenegativeof
the modifier. The real number modifier gives the value of the dipole polarizability in ≈3. The final
integermodifierslisttheatomtypenumbersofatomsdirectlybondedtothecurrentatomandwhich
willbeconsideredtobepartofthecurrentatom'spolarizationgroup.
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POLARIZETERM [NONE/ONLY] This keyword controls use of the atomic dipole polarization
potential energy term. In the absence of a modifying option, this keyword turns on use of the
potential.TheNONEoptionturnsoffuseofthispotentialenergyterm.TheONLYoptionturnsoffall
potentialenergytermsexceptforthisone.
POLYMER-CUTOFF [real] Sets the value of an additional cutoff parameter needed for infinite
polymer systems. This value must be set to less than half the minimal periodic box dimension and
should be greater than the largest possible interatomic distance that can be subject to scaling or
exclusion as a local electrostatic or van der Waals interaction. The default in the absence of the
POLYMER-CUTOFFkeywordis5.5Angstroms.
PRINTOUT[integer]Ageneralparameterforiterativeproceduressuchasminimizationsthatsets
the number of iterations between writes of status information to the standard output. The default
valueintheabsenceofthekeywordis1,i.e.,thecalculationstatusisgiveneveryiteration.
RADIUSRULE[ARITHMETIC/GEOMETRIC/CUBIC-MEAN]Setsthefunctionalformoftheradius
combining rule for heteroatomic van der Waals potential energy interactions. The default in the
absence of the RADIUSRULE keyword is to use the arithmetic mean combining rule to get radii for
heteroatomicinteractions.
RADIUSSIZE [RADIUS/DIAMETER] Determines whether the atom size values given in van der
WaalsparametersreadfromVDWkeywordstatementsareinterpretedasatomicradiusordiameter
values.ThedefaultintheabsenceoftheRADIUSSIZEkeywordistoassumethatvdwsizeparameters
aregivenasradiusvalues.
RADIUSTYPE [R-MIN/SIGMA] Determines whether atom size values given in van der Waals
parametersreadfromVDWkeywordstatementsareinterpretedaspotentialminimum(Rmin)orLJstylesigma(σ)values.ThedefaultintheabsenceoftheRADIUSTYPEkeywordistoassumethatvdw
sizeparametersaregivenasRminvalues.
RANDOMSEED[integer]Followedbyanintegervalue,thiskeywordsetstheinitialseedvaluefor
the random number generator used by TINKER. Setting RANDOMSEED to the same value as an
earlierrunwillallowexactreproductionoftheearliercalculation.(Notethatthiswillnotholdacross
differentmachinetypes.)RANDOMSEEDshouldbesettoapositiveintegerlessthanabout2billion.
IntheabsenceoftheRANDOMSEEDkeywordtheseedischosen``randomly''baseduponthenumber
ofsecondsthathaveelapsedinthecurrentdecade.
RATTLE [BONDS/ANGLES/DIATOMIC/TRIATOMIC/WATER] Invokes the rattle algorithm, a
velocityversionofshake,onportionsofamolecularsystemduringamoleculardynamiccalculation.
TheRATTLEkeywordcanbefollowedbyanyofthemodifiersshown,inwhichcasealloccurrences
ofthemodifierspeciesareconstrainedatidealvaluestakenfromthebondandangleparametersof
theforcefieldinuse.Intheabsenceofanymodifier,RATTLEconstrainsallbondstohydrogenatoms
atidealbondlengths.
RATTLE-DISTANCE [2 integers] This keyword allows the use of a ``Rattle'' constraint between
thetwoatomswhosenumbersarespecifiedonthekeywordline.Ifthetwoatomsareinvolvedina
covalent bond, then their distance is constrained to the ideal bond length from the force field. For
nonbondedatoms,therattleconstraintisfixedattheirdistanceintheinputcoordinatefile.
RATTLE-LINE[integer]Thiskeyword
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RATTLE-ORIGIN[integer]Thiskeyword
RATTLE-PLANE[integer]Thiskeyword
REACTIONFIELD [2 reals & 1 integer] This keyword provides parameters needed for the
reaction field potential energy calculation. The two real modifiers give the radius of the dielectric
cavity and the ratio of the bulk dielectric outside the cavity to that inside the cavity. The integer
modifiergivesthenumberoftermsinthereactionfieldsummationtobeused.Intheabsenceofthe
REACTIONFIELDkeyword,thedefaultvaluesareacavityofradius1000000≈,adielectricratioof80
anduseofonlythefirsttermofthereactionfieldsummation.
REDUCE[real]Specifiesthefractionbetweenzeroandonebywhichthepathbetweenstarting
andfinalconformationalstatewillbeshortenedateachmajorcycleofthetransitionstatelocation
algorithmimplementedbytheSADDLEprogram.Thiscausesthepathendpointstomoveupandout
oftheterminalstructurestowardthetransitionstateregion.Infavorablecases,anonzerovalueof
theREDUCEmodifiercanspeedconvergencetothetransitionstate.Thedefaultvalueintheabsence
oftheREDUCEkeywordiszero.
RESTRAIN-ANGLE [3 integers & 3 reals] This keyword implements a flat-welled harmonic
potentialthatcanbeusedtorestraintheanglebetweenthreeatomstoliewithinaspecifiedangle
range. The integer modifiers contain the atom numbers of the three atoms whose angle is to be
restrained.Thefirstrealmodifieristheforceconstantinkcal/degree2fortherestraint.Thelasttwo
realmodifiersgivethelowerandupperboundsindegreesontheallowedanglevalues.Iftheangle
lies between the lower and upper bounds, the restraint potential is zero. Outside the bounds, the
harmonicrestraintisapplied.Iftheanglerangemodifiersareomitted,thentheatomsarerestrained
totheanglefoundintheinputstructure.Iftheforceconstantisalsoomitted,adefaultvalueof10.0is
used.
RESTRAIN-DISTANCE [2 integers & 3 reals] This keyword implements a flat-welled harmonic
potentialthatcanbeusedtorestraintwoatomstoliewithinaspecifieddistancerange.Theinteger
modifiers contain the atom numbers of the two atoms to be restrained. The first real modifier
specifies the force constant in kcal/≈2 for the restraint. The next two real modifiers give the lower
and upper bounds in ≈ngstroms on the allowed distance range. If the interatomic distance lies
between these lower and upper bounds, the restraint potential is zero. Outside the bounds, the
harmonic restraint is applied. If the distance range modifiers are omitted, then the atoms are
restrained to the interatomic distance found in the input structure. If the force constant is also
omitted,adefaultvalueof100.0isused.
RESTRAIN-GROUPS [2 integers & 3 reals] This keyword implements a flat-welled harmonic
distancerestraintbetweenthecenters-of-massoftwogroupsofatoms.Theintegermodifiersarethe
numbersofthetwogroupswhichmustbedefinedseparatelyviatheGROUPkeyword.Thefirstreal
modifieristheforceconstantinkcal/≈2fortherestraint.Thelasttworealmodifiersgivethelower
and upper bounds in ≈ngstroms on the allowed intergroup center-of-mass distance values. If the
distance range modifiers are omitted, then the groups are restrained to the distance found in the
inputstructure.Iftheforceconstantisalsoomitted,adefaultvalueof100.0isused.
RESTRAIN-POSITION [1 integer & 5 reals] This keyword provides the ability to restrain an
individual atom to a specified coordinate position. The initial integer modifier contains the atom
numberoftheatomtoberestrained.Thefirstrealmodifiersetstheforceconstantinkcal/≈2forthe
harmonicrestraintpotential.ThenextthreerealnumbermodifiersgivetheX-,Y-andZ-coordinates
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to which the atom is tethered. The final real modifier defines a sphere around the specified
coordinates within which the restraint value is zero. If the exclusion sphere radius is omitted, it is
takentobezero.Ifthecoordinatesareomitted,thentheatomisrestrainedtotheorigin.Iftheforce
constantisalsoomitted,adefaultvalueof100.0isused.
RESTRAIN-TORSION [4 integers & 3 reals] This keyword implements a flat-welled harmonic
potentialthatcanbeusedtorestrainthetorsionalanglebetweenfouratomstoliewithinaspecified
angle range. The initial integer modifiers contains the atom numbers of the four atoms whose
torsionalangle,computedintheatomorderlisted,istoberestrained.Thefirstrealmodifiergivesa
forceconstantinkcal/degree2fortherestraint.Thelasttworealmodifiersgivethelowerandupper
bounds in degrees on the allowed torsional angle values. The angle values given can wrap around
across-180and+180degrees.Outsidetheallowedanglerange,theharmonicrestraintisapplied.If
theanglerangemodifiersareomitted,thentheatomsarerestrainedtothetorsionalanglefoundin
theinputstructure.Iftheforceconstantisalsoomitted,adefaultvalueof1.0isused.
RESTRAINTERM [NONE/ONLY] This keyword controls use of the restraint potential energy
terms.Intheabsenceofamodifyingoption,thiskeywordturnsonuseofthesepotentials.TheNONE
optionturnsoffuseofthesepotentialenergyterms.TheONLYoptionturnsoffallpotentialenergy
termsexceptfortheseterms.
RXNFIELDTERM [NONE/ONLY] This keyword controls use of the reaction field continuum
solvationpotentialenergyterm.Intheabsenceofamodifyingoption,thiskeywordturnsonuseof
thepotential.TheNONEoptionturnsoffuseofthispotentialenergyterm.TheONLYoptionturnsoff
allpotentialenergytermsexceptforthisone.
SADDLEPOINT The presence of this keyword allows Newton-style second derivative-based
optimizationroutineusedbyNEWTON,NEWTROTandotherprogramstoconvergetosaddlepoints
aswellasminimaonthepotentialsurface.Bydefault,intheabsenceoftheSADDLEPOINTkeyword,
checks are applied that prevent convergence to stationary points having directions of negative
curvature.
SAVE-CYCLE This keyword causes TINKER programs, such as minimizations, that output
intermediate coordinate sets to save each successive set to the next consecutively numbered cycle
file.TheSAVE-CYCLEkeywordistheoppositeoftheOVERWRITEkeyword.
SAVE-FORCEThiskeywordcausesTINKERmoleculardynamicscalculationstosavethevaluesof
the force components on each atom to a separate cycle file. These files are written whenever the
atomic coordinate snapshots are written during the dynamics run. Each atomic force file name
containsasasuffixthecyclenumberfollowedbytheletterf.
SAVE-INDUCED This keyword causes TINKER molecular dynamics calculations that involve
polarizable atomic multipoles to save the values of the induced dipole components on each
polarizable atom to a separate cycle file. These files are written whenever the atomic coordinate
snapshotsarewrittenduringthedynamicsrun.Eachinduceddipolefilenamecontainsasasuffixthe
cyclenumberfollowedbytheletteru.
SAVE-VELOCITYThiskeywordcausesTINKERmoleculardynamicscalculationstosavethevalues
ofthevelocitycomponentsoneachatomtoaseparatecyclefile.Thesefilesarewrittenwheneverthe
atomiccoordinatesnapshotsarewrittenduringthedynamicsrun.Eachvelocityfilenamecontains
asasuffixthecyclenumberfollowedbytheletterv.
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SLOPEMAX[real]Thiskeywordanditsmodifyingvaluesetthemaximumallowedsizeoftheratio
between the current and initial projected gradients during the line search phase of conjugate
gradient or truncated Newton optimizations. If this ratio exceeds SLOPEMAX, then the initial step
sizeisreducedbyafactorof10.Thedefaultvalueisusuallysetto10000.0whennotspecifiedviathe
SLOPEMAXkeyword.
SMOOTHING [DEM/GDA/TOPHAT/STOPHAT] This keyword activates the potential energy
smoothing methods. Several variations are available depending on the value of the modifier used:
DEM= Diffusion Equation Method with a standard Gaussian kernel; GDA= Gaussian Density
AnnealingasproposedbytheStraubgroup;TOPHAT=alocalDEM-likemethodusingafiniterange
``tophat''kernel;STOPHAT=shiftedtophatsmoothing.
SOLVATE [ASP/SASA/ONION/STILL/HCT/ACE/GBSA] Use of this keyword during energy
calculations with any of the standard force fields turns on a continuum solvation free energy term.
Severalalgorithmsareavailablebasedonthemodifierused:ASP=Eisenberg-McLachlanASPmethod
using the Wesson-Eisenberg vacuum-to-water parameters; SASA= the Ooi-Scheraga SASA method;
ONION= the original 1990 Still ``Onion-shell'' GB/SA method; STILL= the 1997 analytical GB/SA
methodfromStill'sgroup;HCT=thepairwisedescreeningmethodofHawkins,CramerandTruhlar;
ACE= the Analytical Continuum Electrostatics solvation method from the Karplus group; GBSA=
equivalenttotheSTILLmodifier.Atpresent,GB/SA-stylemethodsareonlyvalidforforcefieldsthat
usesimplepartialchargeelectrostatics.
SOLVATETERM[NONE/ONLY]Thiskeywordcontrolsuseofthemacroscopicsolvationpotential
energy term. In the absence of a modifying option, this keyword turns on use of the potential. The
NONE option turns off use of this potential energy term. The ONLY option turns off all potential
energytermsexceptforthisone.
SPACEGROUP[name]Thiskeywordselectsthespacegrouptobeusedinmanipulationofcrystal
unitcellsandasymmetricunits.Thenameoptionmustbechosenfromoneofthefollowingcurrently
implemented space groups: P1, P1(-), P21, Cc, P21/a, P21/n, P21/c, C2/c, P212121, Pna21, Pn21a,
Cmc21,Pccn,Pbcn,Pbca,P41,I41/a,P4(-)21c,P4(-)m2,R3c,P6(3)/mcm,Fm3(-)m,Im3(-)m.
SPHERE[4reals,or1integer&1real]ThiskeywordprovidesanalternativetotheACTIVEand
INACTIVE keywords for specification of subsets of active atoms. If four real number modifiers are
provided,thefirstthreearetakenasX-,Y-andZ-coordinatesandthefourthistheradiusofasphere
centeredatthesecoordinates.Inthiscase,allatomswithinthesphereatthestartofthecalculation
areactivethroughoutthecalculation,whileallotheratomsareinactive.Similarlyifoneintegerand
realnumberaregiven,an``active''spherewithradiussetbytherealiscenteredonthesystematom
withatomnumbergivenbytheintegermodifier.MultipleSPHEREkeywordlinescanbepresentina
singlekeyfile,andthelistofactiveatomsspecifiedbythespheresiscumulative.
STEEPEST-DESCENTThiskeywordforcestheL-BFGSoptimizationroutineusedbytheMINIMIZE
programandotherprogramstoperformsteepestdescentminimization.Thisoptioncanbeusefulin
conjunctionwithsmallstepsizesforfollowingminimumenergypaths,butisgenerallyinferiortothe
L-BFGSdefaultformostoptimizationpurposes.
STEPMAX[real]Thiskeywordanditsmodifyingvaluesetthemaximumsizeofanindividualstep
duringthelinesearchphaseofconjugategradientortruncatedNewtonoptimizations.Thestepsize
iscomputedasthenormofthevectorofchangesinparametersbeingoptimized.Thedefaultvalue
depends on the particular TINKER program, but is usually in the range from 1.0 to 5.0 when not
specifiedviatheSTEPMAXkeyword.
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STEPMIN[real]Thiskeywordanditsmodifyingvaluesettheminimumsizeofanindividualstep
duringthelinesearchphaseofconjugategradientortruncatedNewtonoptimizations.Thestepsize
iscomputedasthenormofthevectorofchangesinparametersbeingoptimized.Thedefaultvalueis
usuallysettoabout10-16whennotspecifiedviatheSTEPMINkeyword.
STRBND[1integer&3reals]Thiskeywordprovidesthevaluesforasinglestretch-bendcross
termpotentialparameter.Theintegermodifiergivestheatomclassnumberforthecentralatomof
the bond angle involved in stretch-bend interactions. The real number modifiers give the force
constant values to be used when the central atom of the angle is attached to 0, 1 or 2 additional
hydrogenatoms,respectively.Thedefaultunitsforthestretch-bendforceconstantarekcal/mole/≈degree,butthiscanbecontrolledviatheSTRBNDUNITkeyword.
STRBNDTERM [NONE/ONLY] This keyword controls use of the bond stretching-angle bending
crosstermpotentialenergy.Intheabsenceofamodifyingoption,thiskeywordturnsonuseofthe
potential.TheNONEoptionturnsoffuseofthispotentialenergyterm.TheONLYoptionturnsoffall
potentialenergytermsexceptforthisone.
STRBNDUNIT [real] Sets the scale factor needed to convert the energy value computed by the
bondstretching-anglebendingcrosstermpotentialintounitsofkcal/mole.Thecorrectvalueisforce
field dependent and typically provided in the header of the master force field parameter file. The
defaultvalueof1.0isused,iftheSTRBNDUNITkeywordisnotgivenintheforcefieldparameterfile
orthekeyfile.
STRTORS [2 integers & 1 real] This keyword provides the values for a single stretch-torsion
crosstermpotentialparameter.Thetwointegermodifiersgivetheatomclassnumbersfortheatoms
involvedinthecentralbondofthetorsionalanglestobeparameterized.Therealmodifiergivesthe
valueofthestretch-torsionforceconstantforalltorsionalangleswiththedefinedcentralbondatom
classes. The default units for the stretch-torsion force constant can be controlled via the
STRTORUNITkeyword.
STRTORTERM [NONE/ONLY] This keyword controls use of the bond stretching-torsional angle
crosstermpotentialenergy.Intheabsenceofamodifyingoption,thiskeywordturnsonuseofthe
potential.TheNONEoptionturnsoffuseofthispotentialenergyterm.TheONLYoptionturnsoffall
potentialenergytermsexceptforthisone.
STRTORUNIT [real] Sets the scale factor needed to convert the energy value computed by the
bond stretching-torsional angle cross term potential into units of kcal/mole. The correct value is
force field dependent and typically provided in the header of the master force field parameter file.
Thedefaultvalueof1.0isused,iftheSTRTORUNITkeywordisnotgivenintheforcefieldparameter
fileorthekeyfile.
TAPER [real] This keyword allows modification of the cutoff windows for nonbonded potential
energy interactions. The nonbonded terms are smoothly reduced from their standard value at the
beginning of the cutoff window to zero at the far end of the window. The far end of the window is
specified via the CUTOFF keyword or its potential function specific variants. The modifier value
suppliedwiththeTAPERkeywordsetsthebeginningofthecutoffwindow.Themodifiercanbegiven
either as an absolute distance value in Angstroms, or as a fraction between zero and one of the
CUTOFFdistance.ThedefaultvalueintheabsenceoftheTAPERkeywordrangesfrom0.65to0.9of
theCUTOFFdistancedependingonthetypeofpotentialfunction.Thewindowsareimplementedvia
polynomial-basedswitchingfunctions,insomecasescombinedwithenergyshifting.
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TAU-PRESSURE[real]SetsthecouplingtimeinpicosecondsfortheGroningen-stylepressurebath
couplingusedtocontrolthesystempressureduringmoleculardynamicscalculations.Adefaultvalue
of2.0isusedforTAU-PRESSUREintheabsenceofthekeyword.
TAU-TEMPERATURE [real] Sets the coupling time in picoseconds for the Groningen-style
temperature bath coupling used to control the system temperature during molecular dynamics
calculations.Adefaultvalueof0.1isusedforTAU-TEMPERATUREintheabsenceofthekeyword.
THERMOSTAT[BERENDSEN/ANDERSEN]Thiskeywordselectsathermostatalgorithmforuse
duringmoleculardynamics.Twomodifiersareavailable,aBerendsenbathcouplingmethod,andan
Andersenstochasticcollisionmethod.ThedefaultintheabsenceoftheTHERMOSTATkeywordisto
usetheBERENDSENalgorithm.
TORSION[4integers&upto6real/real/integertriples]Thiskeywordprovidesthevaluesfor
asingletorsionalangleparameter.Thefirstfourintegermodifiersgivetheatomclassnumbersfor
the atoms involved in the torsional angle to be defined. Each of the remaining triples of
real/real/integermodifiersgivetheamplitude,phaseoffsetindegreesandperiodicityofaparticular
torsional function term, respectively. Periodicities through 6-fold are allowed for torsional
parameters.
TORSION4[4integers&upto6real/real/integertriples]Thiskeywordprovidesthevaluesfor
a single torsional angle parameter specific to atoms in 4-membered rings. The first four integer
modifiers give the atom class numbers for the atoms involved in the torsional angle to be defined.
The remaining triples of real number and integer modifiers operate as described above for the
TORSIONkeyword.
TORSION5[4integers&upto6real/real/integertriples]Thiskeywordprovidesthevaluesfor
a single torsional angle parameter specific to atoms in 5-membered rings. The first four integer
modifiers give the atom class numbers for the atoms involved in the torsional angle to be defined.
The remaining triples of real number and integer modifiers operate as described above for the
TORSIONkeyword.
TORSIONTERM[NONE/ONLY]Thiskeywordcontrolsuseofthetorsionalanglepotentialenergy
term. In the absence of a modifying option, this keyword turns on use of the potential. The NONE
option turns off use of this potential energy term. The ONLY option turns off all potential energy
termsexceptforthisone.
TORSIONUNIT[real]Sets the scale factor needed to convert the energy value computed by the
torsional angle potential into units of kcal/mole. The correct value is force field dependent and
typically provided in the header of the master force field parameter file. The default value of 1.0 is
used,iftheTORSIONUNITkeywordisnotgivenintheforcefieldparameterfileorthekeyfile.
TORTOR [7 integers, then multiple lines of 2 integers and 1 real] This keyword is used to
provide the values for a single torsion-torsion parameter. The first five integer modifiers give the
atom class numbers for the atoms involved in the two adjacent torsional angles to be defined. The
last two integer modifiers contain the number of data grid points that lie along each axis of the
torsion-torsionmap.Forexample,thisvaluewillbe13fora30degreetorsionalanglespacing, i.e.,
360/30=12,but13valuesarerequiredsincedatavaluesfor-180and+180degreesmustbothbe
supplied.Thesubsequentlinescontainthetorsion-torsionmapdataastheintegervaluesindegrees
ofeachtorsionalangleandthetargetenergyvalueinkcal/mole.
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TORTORTERM[NONE/ONLY]Thiskeywordcontrolsuseofthetorsion-torsionpotentialenergy
term. In the absence of a modifying option, this keyword turns on use of the potential. The NONE
option turns off use of this potential energy term. The ONLY option turns off all potential energy
termsexceptforthisone.
TORTORUNIT [real] Sets the scale factor needed to convert the energy value computed by the
torsion-torsion potential into units of kcal/mole. The correct value is force field dependent and
typically provided in the header of the master force field parameter file. The default value of 1.0 is
used,iftheTORTORUNITkeywordisnotgivenintheforcefieldparameterfileorthekeyfile.
TRIAL-DISTANCE[CLASSIC/RANDOM/TRICOR/HAVELinteger/PAIRWISEinteger]Sets
the method for selection of a trial distance matrix during distance geometry computations. The
keyword takes a modifier that selects the method to be used. The HAVEL and PAIRWISE modifiers
alsorequireanadditionalintegervaluethatspecifiesthenumberofatomsusedinmetrizationand
thepercentageofmetrization,respectively.Thedefaultintheabsenceofthiskeywordistousethe
PAIRWISE method with 100 percent metrization. Further information on the various methods is
givenwiththedescriptionoftheTINKERdistancegeometryprogram.
TRIAL-DISTRIBUTION[real]SetstheinitialvalueforthemeanoftheGaussiandistributionused
to select trial distances between the lower and upper bounds during distance geometry
computations. The value given must be between 0 and 1 which represent the lower and upper
bounds respectively. This keyword is rarely needed since TINKER will usually be able to choose a
reasonablevaluebydefault.
TRUNCATECausesalldistance-basednonbondenergycutoffstobesharplytruncatedtoanenergy
ofzeroatdistancesgreaterthanthevaluesetbythecutoffkeyword(s)withoutuseofanyshifting,
switchingorsmoothingschemes.Atalldistanceswithinthecutoffsphere,thefullinteractionenergy
iscomputed.
UREY-CUBIC [real] Sets the value of the cubic term in the Taylor series expansion form of the
Urey-Bradley potential energy. The real number modifier gives the value of the coefficient as a
multipleofthequadraticcoefficient.ThedefaultvalueintheabsenceoftheUREY-CUBICkeywordis
zero;i.e.,thecubicUrey-Bradleytermisomitted.
UREY-QUARTIC[real]SetsthevalueofthequartictermintheTaylorseriesexpansionformofthe
Urey-Bradley potential energy. The real number modifier gives the value of the coefficient as a
multipleofthequadraticcoefficient.ThedefaultvalueintheabsenceoftheUREY-QUARTICkeyword
iszero;i.e.,thequarticUrey-Bradleytermisomitted.
UREYBRAD [3 integers & 2 reals] This keyword provides the values for a single Urey-Bradley
cross term potential parameter. The integer modifiers give the atom class numbers for the three
kindsofatomsinvolvedintheangleforwhichaUrey-Bradleytermistobedefined.Therealnumber
modifiersgivetheforceconstantvalueforthetermandthetargetvalueforthe1-3distancein≈.The
default units for the force constant are kcal/mole/≈2, but this can be controlled via the UREYUNIT
keyword.
UREYTERM[NONE/ONLY]ThiskeywordcontrolsuseoftheUrey-Bradleypotentialenergyterm.
Intheabsenceofamodifyingoption,thiskeywordturnsonuseofthepotential.TheNONEoption
turns off use of this potential energy term. The ONLY option turns off all potential energy terms
exceptforthisone.
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UREYUNIT[real]SetsthescalefactorneededtoconverttheenergyvaluecomputedbytheUreyBradley potential into units of kcal/mole. The correct value is force field dependent and typically
providedintheheaderofthemasterforcefieldparameterfile.Thedefaultvalueof1.0isused,ifthe
UREYUNITkeywordisnotgivenintheforcefieldparameterfileorthekeyfile.
VDW[1integer&3reals]ThiskeywordprovidesvaluesforasinglevanderWaalsparameter.
The integer modifier, if positive, gives the atom class number for which vdw parameters are to be
defined.Notethatvdwparametersaregivenforatomclasses,notatomtypes.Thethreerealnumber
modifiersgivethevaluesoftheatomsizein≈,homoatomicwelldepthinkcal/mole,andanoptional
reductionfactorforunivalentatoms.
VDW-12-SCALE[real]Thiskeywordprovidesamultiplicativescalefactorthatisappliedtovan
derWaalspotentialinteractionsbetween1-2connectedatoms,i.e.,atomsthataredirectlybonded.
Thedefaultvalueof0.0isused,iftheVDW-12-SCALEkeywordisnotgivenineithertheparameter
fileorthekeyfile.
VDW-13-SCALE[real]Thiskeywordprovidesamultiplicativescalefactorthatisappliedtovan
derWaalspotentialinteractionsbetween1-3connectedatoms,i.e.,atomsseparatedbytwocovalent
bonds. The default value of 0.0 is used, if the VDW-13-SCALE keyword is not given in either the
parameterfileorthekeyfile.
VDW-14-SCALE[real]Thiskeywordprovidesamultiplicativescalefactorthatisappliedtovan
der Waals potential interactions between 1-4 connected atoms, i.e., atoms separated by three
covalentbonds.Thedefaultvalueof1.0isused,iftheVDW-14-SCALEkeywordisnotgivenineither
theparameterfileorthekeyfile.
VDW-15-SCALE[real]Thiskeywordprovidesamultiplicativescalefactorthatisappliedtovan
derWaalspotentialinteractionsbetween1-5connectedatoms,i.e.,atomsseparatedbyfourcovalent
bonds. The default value of 1.0 is used, if the VDW-15-SCALE keyword is not given in either the
parameterfileorthekeyfile.
VDW-CUTOFF [real] Sets the cutoff distance value in Angstroms for van der Waals potential
energyinteractions.TheenergyforanypairofvanderWaalssitesbeyondthecutoffdistancewillbe
settozero.Otherkeywordscanbeusedtoselectasmoothingschemenearthecutoffdistance.The
default cutoff distance in the absence of the VDW-CUTOFF keyword is infinite for nonperiodic
systemsand9.0forperiodicsystems.
VDW-TAPER [real] This keyword allows modification of the cutoff windows for van der Waals
potentialenergyinteractions.ItissimilarinformandactiontotheTAPERkeyword,exceptthatits
valueappliesonlytothevdwpotential.ThedefaultvalueintheabsenceoftheVDW-TAPERkeyword
istobeginthecutoffwindowat0.9ofthevdwcutoffdistance.
VDW14[1integer&2reals]ThiskeywordprovidesvaluesforasinglevanderWaalsparameter
forusein1-4nonbondedinteractions.Theintegermodifier,ifpositive,givestheatomclassnumber
forwhichvdwparametersaretobedefined.Notethatvdwparametersaregivenforatomclasses,
not atom types. The two real number modifiers give the values of the atom size in ≈ and the
homoatomic well depth in kcal/mole. Reduction factors, if used, are carried over from the VDW
keywordforthesameatomclass.
VDWPR[2integers&2reals]Thiskeywordprovidesthevaluesforthevdwparametersfora
singlespecialheteroatomicpairofatoms.Theintegermodifiersgivethepairofatomclassnumbers
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forwhichspecialvdwparametersaretobedefined.Thetworealnumbermodifiersgivethevaluesof
theminimumenergycontactdistancein≈andthewelldepthattheminimumdistanceinkcal/mole.
VDWTERM[NONE/ONLY]ThiskeywordcontrolsuseofthevanderWaalsrepulsion-dispersion
potential energy term. In the absence of a modifying option, this keyword turns on use of the
potential.TheNONEoptionturnsoffuseofthispotentialenergyterm.TheONLYoptionturnsoffall
potentialenergytermsexceptforthisone.
VDWTYPE [LENNARD-JONES / BUCKINGHAM / BUFFERED-14-7 / MM3-HBOND / GAUSSIAN]
Sets the functional form for the van der Waals potential energy term. The text modifier gives the
name of the functional form to be used. The GAUSSIAN modifier value implements a two or four
Gaussian fit to the corresponding Lennard-Jones function for use with potential energy smoothing
schemes.ThedefaultintheabsenceoftheVDWTYPEkeywordistousethestandardtwoparameter
Lennard-Jonesfunction.
VERBOSE Turns on printing of secondary and informational output during a variety of TINKER
computations;asubsetofthemoreextensiveoutputprovidedbytheDEBUGkeyword.
WALL [real] Sets the radius of a spherical boundary used to maintain droplet boundary
conditions.Therealmodifierspecifiesthedesiredapproximateradiusofthedroplet.Inpractice,an
artificial van der Waals wall is constructed at a fixed buffer distance of 2.5 ≈ outside the specified
radius. The effect is that atoms which attempt to move outside the region defined by the droplet
radiuswillbeforcedtowardthecenter.
WRITEOUT [integer] A general parameter for iterative procedures such as minimizations that
sets the number of iterations between writes of intermediate results (such as the current
coordinates)todiskfile(s).Thedefaultvalueintheabsenceofthekeywordis1,i.e.,theintermediate
results are written to file on every iteration. Whether successive intermediate results are saved to
new files or replace previously written intermediate results is controlled by the OVERWRITE and
SAVE-CYCLEkeywords.
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8.
ForceFieldParameterSets
TheTINKERpackageisdistributedwithseveralforcefieldparametersets,implementingaselection
ofwidelyusedliteratureforcefieldsaswellastheTINKERforcefieldcurrentlyunderconstructionin
the Ponder lab. We try to exactly reproduce the intent of the original authors of our distributed,
third-partyforcefields.Inallcasestheparametersetshavebeenvalidatedagainstliteraturereports,
resultsprovidedbytheoriginaldevelopers,orcalculationsmadewiththeauthenticprograms.With
the few exceptions noted below, TINKER calculations can be treated as authentic results from the
genuineforcefields.Abriefdescriptionofeachparameterset,includingsomestillinpreparationand
not distributed with the current version, is provided below with lead literature references for the
forcefield:
AMOEBA.PRM
Parameters for the AMOEBA polarizable atomic multipole force field. As of the current TINKER
release,wehavecompletedparametrizationforanumberofionsandsmallorganicmolecules.For
further information, or if you are interested in developing or testing parameters for other small
molecules,pleasecontactthePonderlab.
P. Ren and J. W. Ponder, A Consistent Treatment of Inter- and Intramolecular Polarization in
MolecularMechanicsCalculations,J.Comput.Chem.,23,1497-1506(2002)
P. Ren and J. W. Ponder, Polarizable Atomic Multipole Water Model for Molecular Mechanics
Simulation,J.Phys.Chem.B,107,5933-5947(2003)
P. Ren and J. W. Ponder, Ion Solvation Thermodynamics from Simulation with a Polarizable Force
Field,A.Grossfield,J.Am.Chem.Soc.,125,15671-15682(2003)
AMOEBAPRO.PRM
PreliminaryproteinparametersfortheAMOEBApolarizableatomicmultipoleforcefield.Whilethe
distributedparametersarestillsubjecttominoralterationaswecontinuevalidation,theyarenow
stableenoughforothergroupstobeginusingthem.Forfurtherinformation,orifyouareinterested
intestingtheproteinparameterset,pleasecontactthePonderlab.
J.W.PonderandD.A.Case,ForceFieldsforProteinSimulation,Adv.Prot.Chem.,66,27-85(2003)
P.RenandJ.W.Ponder,PolarizableAtomicMultipole-basedPotentialforProteins:Modeland
Parameterization,inpreparation
AMBER94.PRM
AMBERff94parametersforproteinsandnucleicacids.Notethatwiththeir``Cornell''forcefield,the
Kollmangrouphasdevisedseparate,fullyindependentpartialchargevaluesforeachoftheN-andCterminalaminoacidresidues.Atpresent,theterminalresiduechargesforTINKER'sversionmaintain
thecorrectformalcharge,butredistributedsomewhatatthealphacarbonatomsfromtheoriginal
Kollmangroupvalues.Thetotalmagnitudeoftheredistributionislessthan0.01electronsinmost
cases.
W.D.Cornell,P.Cieplak,C.I.Bayly,I.R.Gould,K.M.Merz,Jr.,D.M.Ferguson,D.C.Spellmeyer,T.Fox,
J. W. Caldwell and P. A. Kollman, A Second Generation Force Field for the Simulation of Proteins,
NucleicAcids,andOrganicMolecules,J.Am.Chem.Soc.,117,5179-5197(1995)[ff94]
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G. Moyna, H. J. Williams, R. J. Nachman and A. I. Scott, Conformation in Solution and Dynamics of a
Structurally Constrained Linear Insect Kinin Pentapeptide Analogue, Biopolymers, 49, 403-413
(1999)[AIBcharges]
W. S. Ross and C. C. Hardin, Ion-Induced Stabilization of the G-DNA Quadruplex: Free Energy
PerturbationStudies,J.Am.Chem.Soc.,116,4363-4366(1994)[alkalimetalions]
J. Aqvist, Ion-Water Interaction Potentials Derived from Free Energy Perturbation Simulations, J.
Phys.Chem.,94,8021-8024,1990[alkalineearthIons,radiiadaptedforAmbercombiningrule]
Current force field parameter values and suggested procedures for development of parameters for
additional molecules are available from the Amber web site in the Case lab at Scripps,
http://amber.scripps.edu/
AMBER96.PRM
AMBERff96parametersforproteinsandnucleicacids.Theonlychangefromtheff94parameterset
isinthetorsionalparametersfortheproteinphi/psiangles.Thesevalueswerealteredtogivebetter
agreement with changes of ff96 with LMP2 QM results from the Friesner lab on alanine dipeptide
andtetrapeptide.
P.Kollman,R.Dixon,W.Cornell,T.Fox,C.ChipotandA.Pohorille,TheDevelopment/Applicationofa
'Minimalist' Organic/Biochemical Molecular Mechanic Force Field using a Combination of ab Initio
CalculationsandExperimentalData,inComputerSimulationofBiomolecularSystems,W.F.van
Gunsteren,P.K.Weiner,A.J.Wilkinson,eds.,Volume3,83-96(1997)[ff96]
Current force field parameter values and suggested procedures for development of parameters for
additional molecules are available from the Amber web site in the Case lab at Scripps,
http://amber.scripps.edu/
AMBER98.PRM
AMBERff98parametersforproteinsandnucleicacids.Theonlychangefromtheff94parameterset
isintheglycosidictorsionalparametersthatcontrolsugarpucker.
T.E.CheathamIII,P.CieplakandP.A.Kollman,AModifiedVersionoftheCornelletal.ForceField
withImprovedSugarPuckerPhasesandHelicalRepeat,J.Biomol.Struct.Dyn.,16,845-862(1999)
Current force field parameter values and suggested procedures for development of parameters for
additional molecules are available from the Amber web site in the Case lab at Scripps,
http://amber.scripps.edu/
AMBER99.PRM
AMBER ff99 parameters for proteins and nucleic acids. The original partial charges from the ff94
parametersetareretained,butmanyofthebond,angleandtorsionalparametershavebeenrevised
toprovidebettergeneralagreementwithexperiment.
J. Wang, P. Cieplak and P. A. Kollman, How Well Does a Restrained Electrostatic Potential (RESP)
Model Perform in Calcluating Conformational Energies of Organic and Biological Molecules?, J.
Comput.Chem.,21,1049-1074(2000)
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Current force field parameter values and suggested procedures for development of parameters for
additional molecules are available from the Amber web site in the Case lab at Scripps,
http://amber.scripps.edu/
CHARMM19.PRM
CHARMM19 united-atom parameters for proteins. The nucleic acid parameter are not yet
implemented. There are some differences between authentic CHARMM19 and the TINKER version
due to replacement of CHARMM impropers by torsions for cases that involve atoms not bonded to
thetrigonalatomandTINKER'suseofallpossibletorsionsacrossabondinsteadofasingletorsion
perbond.
E. Neria, S. Fischer and M. Karplus, Simulation of Activation Free Energies in Molecular Systems, J.
Chem.Phys.,105,1902-1921(1996)
L. Nilsson and M. Karplus, Empirical Energy Functions for Energy Minimizations and Dynamics of
NucleicAcids,J.Comput.Chem.,7,591-616(1986)
W. E. Reiher III, Theoretical Studies of Hydrogen Bonding, Ph.D. Thesis, Department of Chemistry,
HarvardUniversity,Cambridge,MA,1985
CHARMM22.PRM
CHARMM27 all-atom parameters for proteins and lipids. Most of the nucleic acid and small model
compoundparametersarenotyetimplemented.Weplantoprovidetheseadditionalparametersin
duecourse.
N. Foloppe and A. D. MacKerell, Jr., All-Atom Empirical Force Field for Nucleic Acids: 1) Parameter
OptimizationBasedonSmallMoleculeandCondensedPhaseMacromolecularTargetData,J.Comput.
Chem.,21,86-104(2000)[CHARMM27]
N.BanavaliandA.D.MacKerell,Jr.,All-AtomEmpiricalForceFieldforNucleicAcids:2)Application
to Molecular Dynamics Simulations of DNA and RNA in Solution, J. Comput. Chem., 21, 105-120
(2000)
A.D.MacKerrell,Jr.,etal.,All-AtomEmpiricalPotentialforMolecularModelingandDynamicsStudies
ofProteins,J.Phys.Chem.B,102,3586-3616(1998)[CHARMM22]
A.D.MacKerell,Jr.,J.Wiorkeiwicz-KuczeraandM.Karplus,AnAll-AtomEmpiricalEnergyFunction
fortheSimulationofNucleicAcids,J.Am.Chem.Soc.,117,11946-11975(1995)
S. E. Feller, D. Yin, R. W. Pastor and A. D. MacKerell, Jr., Molecular Dynamics Simulation of
Unsaturated Lipids at Low Hydration: Parametrization and Comparison with Diffraction Studies,
BiophysicalJournal,73,2269-2279(1997)[alkenes]
R.H.StoteandM.Karplus,ZincBindinginProteinsandSolution-ASimplebutAccurateNonbonded
Representation,Proteins,23,12-31(1995)[zincion]
Current and legacy parameter values are available from the CHARMM force field web site on Alex
MacKerell's Research Interests page at the University of Maryland School of Pharmacy,
https://rxsecure.umaryland.edu/research/amackere/research.html/
DUDEK.PRM
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Protein-onlyparametersfortheearly1990'sTINKERforcefieldwithmultipolevaluesofDudekand
Ponder. The current file contains only the multipole values from the 1995 paper by Dudek and
Ponder. This set is now superceeded by the more recent TINKER force field developed by Pengyu
Ren(seeWATER.PRM,below).
M. J. Dudek and J. W. Ponder, Accurate Electrostatic Modelling of the Intramolecular Energy of
Proteins,J.Comput.Chem.,16,791-816(1995)
ENCAD.PRM
ENCADparametersforproteinsandnucleicacids.(inpreparation)
M. Levitt, M. Hirshberg, R. Sharon and V. Daggett, Potential Energy Function and Parameters for
Simulations of the Molecular Dynamics of Protein and Nucleic Acids in Solution, Comp. Phys.
Commun.,91,215-231(1995)
M. Levitt, M. Hirshberg, R. Sharon, K. E. Laidig and V. Daggett, Calibration and Testing of a Water
Model for Simulation of the Molecular Dynamics of Protein and Nucleic Acids in Solution, J. Phys.
Chem.B,101,5051-5061(1997)[F3Cwater]
HOCH.PRM
SimpleNMR-NOEforcefieldofHochandStern.
J. C. Hoch and A. S. Stern, A Method for Determining Overall Protein Fold from NMR Distance
Restraints,J.Biomol.NMR,2,535-543(1992)
MM2.PRM
Full MM2(1991) parameters including π-systems. The anomeric and electronegativity correction
termsincludedinsomelaterversionsofMM2arenotimplemented.
N. L. Allinger, Conformational Analysis. 130. MM2. A Hydrocarbon Force Field Utilizing V1 and V2
TorsionalTerms,J.Am.Chem.Soc.,99,8127-8134(1977)
J.T.Sprague,J.C.Tai,Y.YuhandN.L.Allinger,TheMMP2CalculationalMethod,J.Comput.Chem.,8,
581-603(1987)
J. C. Tai and N. L. Allinger, Molecular Mechanics Calculations on Conjugated Nitrogen-Containing
Heterocycles,J.Am.Chem.Soc.,110,2050-2055(1988)
J. C. Tai, J.-H. Lii and N. L. Allinger, A Molecular Mechanics (MM2) Study of Furan, Thiophene, and
RelatedCompounds,J.Comput.Chem.,10,635-647(1989)
N. L. Allinger, R. A. Kok and M. R. Imam, Hydrogen Bonding in MM2, J. Comput. Chem., 9, 591-595
(1988)
L.Norskov-LauritsenandN.L.Allinger,AMolecularMechanicsTreatmentoftheAnomericEffect,J.
Comput.Chem.,5,326-335(1984)
AllparametersdistributedwithTINKERarefromthe``MM2(1991)ParameterSet'',asprovidedby
N.L.Allinger,UniversityofGeorgia
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MM3.PRM
Full MM3(2000) parameters including pi-systems. The directional hydrogen bonding term and
electronegativity bond length corrections are implemented, but the anomeric and Bohlmann
correctiontermsarenotimplemented.
N.L.Allinger,Y.H.YuhandJ.-H.Lii,MolecularMechanics.TheMM3ForceFieldforHydrocarbons.1,
J.Am.Chem.Soc.,111,8551-8566(1989)
J.-H. Lii and N. L. Allinger, Molecular Mechanics. The MM3 Force Field for Hydrocarbons. 2.
VibrationalFrequenciesandThermodynamics,J.Am.Chem.Soc.,111,8566-8575(1989)
J.-H.LiiandN.L.Allinger,MolecularMechanics.TheMM3ForceFieldforHydrocarbons.3.Thevan
derWaals'PotentialsandCrystalDataforAliphaticandAromaticHydrocarbons,J.Am.Chem.Soc.,
111,8576-8582(1989)
N.L.Allinger,H.J.Geise,W.Pyckhout,L.A.PaquetteandJ.C.Gallucci,StructuresofNorbornaneand
Dodecahedrane by Molecular Mechanics Calculations (MM3), X-ray Crystallography, and Electron
Diffraction,J.Am.Chem.Soc.,111,1106-1114(1989)[stretch-torsioncrossterm]
N. L. Allinger, F. Li and L. Yan, Molecular Mechanics. The MM3 Force Field for Alkenes, J. Comput.
Chem.,11,848-867(1990)
N. L. Allinger, F. Li, L. Yan and J. C. Tai, Molecular Mechanics (MM3) Calculations on Conjugated
Hydrocarbons,J.Comput.Chem.,11,868-895(1990)
J.-H. Lii and N. L. Allinger, Directional Hydrogen Bonding in the MM3 Force Field. I, J. Phys. Org.
Chem.,7,591-609(1994)
J.-H.LiiandN.L.Allinger,DirectionalHydrogenBondingintheMM3ForceField.II,J.Comput.Chem.,
19,1001-1016(1998)
AllparametersdistributedwithTINKERarefromthe``MM3(2000)ParameterSet'',asprovidedby
N.L.Allinger,UniversityofGeorgia,August2000
MM3PRO.PRM
Protein-onlyversionoftheMM3parameters.
J.-H. Lii and N. L. Allinger, The MM3 Force Field for Amides, Polypeptides and Proteins, J. Comput.
Chem.,12,186-199(1991)
OPLSUA.PRM
CompleteOPLS-UAwithunited-atomparametersforproteinsandmanyclassesoforganicmolecules.
Explicithydrogensonpolaratomsandaromaticcarbons.
W.L.JorgensenandJ.Tirado-Rives,TheOPLSPotentialFunctionsforProteins.EnergyMinimizations
forCrystalsofCyclicPeptidesandCrambin,J.Am.Chem.Soc.,110,1657-1666(1988)[peptideand
proteins]
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W. L. Jorgensen and D. L. Severance, Aromatic-Aromatic Interactions: Free Energy Profiles for the
BenzeneDimerinWater,Chloroform,andLiquidBenzene,J.Am.Chem.Soc.,112,4768-4774(1990)
[aromatichydrogens]
S.J.Weiner,P.A.Kollman,D.A.Case,U.C.Singh,C.Ghio,G.Alagona,S.Profeta,Jr.andP.Weiner,A
New Force Field for Molecular Mechanical Simulation of Nucleic Acids and Proteins, J. Am. Chem.
Soc.,106,765-784(1984)[united-atom``AMBER/OPLS''localgeometry]
S. J. Weiner, P. A. Kollman, D. T. Nguyen and D. A. Case, An All Atom Force Field for Simulations of
Proteins and Nucleic Acids, J. Comput. Chem., 7, 230-252 (1986) [all-atom "AMBER/OPLS" local
geometry]
L. X. Dang and B. M. Pettitt, Simple Intramolecular Model Potentials for Water, J. Phys. Chem., 91,
3349-3354(1987)[flexibleTIP3PandSPCwater]
W. L. Jorgensen, J. D. Madura and C. J. Swenson, Optimized Intermolecular Potential Functions for
LiquidHydrocarbons,J.Am.Chem.Soc.,106,6638-6646(1984)[hydrocarbons]
W.L.Jorgensen,E.R.Laird,T.B.NguyenandJ.Tirado-Rives,MonteCarloSimulationsofPureLiquid
Substituted Benzenes with OPLS Potential Functions, J. Comput. Chem., 14, 206-215 (1993)
[substitutedbenzenes]
E. M. Duffy, P. J. Kowalczyk and W. L. Jorgensen, Do Denaturants Interact with Aromatic
Hydrocarbons in Water?, J. Am. Chem. Soc., 115, 9271-9275 (1993) [benzene, naphthalene, urea,
guanidinium,tetramethylammonium]
W. L. Jorgensen and C. J. Swenson, Optimized Intermolecular Potential Functions for Amides and
Peptides. Structure and Properties of Liquid Amides, J. Am. Chem. Soc., 106, 765-784 (1984)
[amides]
W. L. Jorgensen, J. M. Briggs and M. L. Contreras, Relative Partition Coefficients for Organic Solutes
form Fluid Simulations, J. Phys. Chem., 94, 1683-1686 (1990) [chloroform, pyridine, pyrazine,
pyrimidine]
J. M. Briggs, T. B. Nguyen and W. L. Jorgensen, Monte Carlo Simulations of Liquid Acetic Acid and
MethylAcetatewiththeOPLSPotentialFunctions,J.Phys.Chem.,95,3315-3322(1991)[aceticacid,
methylacetate]
H. Liu, F. Muller-Plathe and W. F. van Gunsteren, A Force Field for Liquid Dimethyl Sulfoxide and
PhysicalPropertiesofLiquidDimethylSulfoxideCalculatedUsingMolecularDynamicsSimulation,J.
Am.Chem.Soc.,117,4363-4366(1995)[dimethylsulfoxide]
J. Gao, X. Xia and T. F. George, Importance of Bimolecular Interactions in Developing Empirical
PotentialFunctionsforLiquidAmmonia,J.Phys.Chem.,97,9241-9246(1993)[ammonia]
J. Aqvist, Ion-Water Interaction Potentials Derived from Free Energy Perturbation Simulations, J.
Phys.Chem.,94,8021-8024(1990)[metalions]
W. S. Ross and C. C. Hardin, Ion-Induced Stabilization of the G-DNA Quadruplex: Free Energy
PerturbationStudies,J.Am.Chem.Soc.,116,4363-4366(1994)[alkalimetalions]
J. Chandrasekhar, D. C. Spellmeyer and W. L. Jorgensen, Energy Component Analysis for Dilute
AqueousSolutionsofLi+,Na+,F-,andCl-Ions,J.Am.Chem.Soc.,106,903-910(1984)[halideions]
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Most parameters distributed with TINKER are from ``OPLS and OPLS-AA Parameters for Organic
Molecules,Ions,andNucleicAcids''asprovidedbyW.L.Jorgensen,YaleUniversity,October1997
OPLSAA.PRM
OPLS-AA force field with all-atom parameters for proteins and many general classes of organic
molecules.
W. L. Jorgensen, D. S. Maxwell and J. Tirado-Rives, Development and Testing of the OPLS All-Atom
ForceFieldonConformationalEnergeticsandPropertiesofOrganicLiquids,J.Am.Chem.Soc.,117,
11225-11236(1996)
D.S.Maxwell,J.Tirado-RivesandW.L.Jorgensen,AComprehensiveStudyoftheRotationalEnergy
Profiles of Organic Systems by Ab Initio MO Theory, Forming a Basis for Peptide Torsional
Parameters,J.Comput.Chem.,16,984-1010(1995)
W. L. Jorgensen and N. A. McDonald, Development of an All-Atom Force Field for Heterocycles.
PropertiesofLiquidPyridineandDiazenes,THEOCHEM-J.Mol.Struct.,424,145-155(1998)
N. A. McDonald and W. L. Jorgensen, Development of an All-Atom Force Field for Heterocycles.
PropertiesofLiquidPyrrole,Furan,Diazoles,andOxazoles,J.Phys.Chem.B,102,8049-8059(1998)
R.C.RizzoandW.L.Jorgensen,OPLSAll-AtomModelforAmines:ResolutionoftheAmineHydration
Problem,J.Am.Chem.Soc.,121,4827-4836(1999)
M.L.P.Price,D.OstrovskyandW.L.Jorgensen,Gas-PhaseandLiquid-StatePropertiesofEsters,
Nitriles,andNitroCompoundswiththeOPLS-AAForceField,J.Comput.Chem.,22,1340-1352
(2001)
All parameters distributed with TINKER are from ``OPLS and OPLS-AA Parameters for Organic
Molecules,Ions,andNucleicAcids''asprovidedbyW.L.Jorgensen,YaleUniversity,October1997
OPLSAAL.PRM
AnimprovedOPLS-AAparametersetforproteinsinwhichtheonlychangeisareworkingofmanyof
the backbone and sidechain torsional parameters to give better agreement with LMP2 QM
calculations.ThisparametersetisalsoknownasOPLS(2000).
G.A.Kaminsky,R.A.Friesner,J.Tirado-RivesandW.L.Jorgensen,EvaluationandReparametrization
of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical
CalculationsonPeptides,J.Phys.Chem.B,105,6474-6487(2001)
SMOOTH.PRM
VersionofOPLS-UAforusewithpotentialsmoothing.LargelyadaptedlargelyfromstandardOPLSUAparameterswithmodificationstothevdwandimpropertorsionterms.
R.V.Pappu,R.K.HartandJ.W.Ponder,AnalysisandApplicationofPotentialEnergySmoothingand
Search Methods for Global Optimization, J. Phys, Chem. B, 102, 9725-9742 (1998) [smoothing
modifications]
SMOOTHAA.PRM
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VersionofOPLS-AAforusewithpotentialsmoothing.LargelyadaptedlargelyfromstandardOPLSAAparameterswithmodificationstothevdwandimpropertorsionterms.
R.V.Pappu,R.K.HartandJ.W.Ponder,AnalysisandApplicationofPotentialEnergySmoothingand
Search Methods for Global Optimization, J. Phys, Chem. B, 102, 9725-9742 (1998) [smoothing
modifications]
WATER.PRM
TheAMOEBAwaterparametersforapolarizableatomicmultipoleelectrostaticsmodel.Thismodel
isequalorbettertothebestavailablewatermodelsformanybulkandclusterproperties.
P. Ren and J. W. Ponder, A Polarizable Atomic Multipole Water Model for Molecular Mechanics
Simulation,J.Phys.Chem.B,107,5933-5947(2003)
P. Ren and J. W. Ponder, Ion Solvation Thermodynamics from Simulation with a Polarizable Force
Field,A.Grossfield,J.Am.Chem.Soc.,125,15671-15682(2003)
P. Ren and J. W. Ponder, Temperature and Pressure Dependence of the AMOEBA Water Model, J.
Phys.Chem.B,108,xxxx-xxxx(2004)
An earlier version the AMOEBA water model is described in: Yong Kong, Multipole Electrostatic
MethodsforProteinModelingwithReactionFieldTreatment,Biochemistry&MolecularBiophysics,
WashingtonUniversity,St.Louis,August,1997[availablefromhttp://dasher.wustl.edu/ponder/]
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9.
DescriptionsofTINKERRoutines
ThedistributionversionoftheTINKERpackage containsover700separateprograms,subroutines
and functions. This section contains a brief description of the purpose of most of these code units.
Furtherinformationcanbefoundinthecommentslocatedatthetopofeachsourcecodefile.
ACTIVESubroutine
"active"setsthelistofatomsthatareusedduringeachpotentialenergyfunctioncalculation
ADDBASESubroutine
"addbase"buildstheCartesiancoordinatesforasinglenucleicacidbase;coordinatesarereadfrom
the Protein Data Bank file or found from internal coordinates, then atom types are assigned and
connectivitydatagenerated
ADDBONDSubroutine
"addbond"addsentriestotheattachedatomslistinordertogenerateadirectconnectionbetween
twoatoms
ADDSIDESubroutine
"addside" builds the Cartesian coordinates for a single amino acid side chain; coordinates are read
fromtheProteinDataBankfileorfoundfrominternalcoordinates,thenatomtypesareassignedand
connectivitydatagenerated
ADJACENTFunction
"adjacent"findsanatomconnectedtoatom"i1"otherthanatom"i2";ifnosuchatomexists,thenthe
closestatominspaceisreturned
ALCHEMYProgram
"alchemy"computesthefreeenergydifferencecorrespondingtoasmallperturbationbyBoltzmann
weighting the potential energy difference over a number of sample states; current version
(incorrectly)considersthechargeenergytobeintermolecularinfindingtheperturbationenergies
ANALYSISSubroutine
"analysis" calls the series of routines needed to calculate the potential energy and perform energy
partitioninganalysisintermsoftypeofinteractionoratomnumber
ANALYZ4Subroutine
"analyz4" prints the energy to 4 decimal places and number of interactions for each component of
thepotentialenergy
ANALYZ6Subroutine
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"analyz6" prints the energy to 6 decimal places and number of interactions for each component of
thepotentialenergy
ANALYZ8Subroutine
"analyz8" prints the energy to 8 decimal places and number of interactions for each component of
thepotentialenergy
ANALYZEProgram
"analyze"computesanddisplaysthetotalpotential;optionsareprovidedtopartitiontheenergyby
atomorbypotentialfunctiontype;parametersusedincomputinginteractionscanalsobedisplayed
byatom;outputoflargeenergyinteractionsandofelectrostaticandinertialpropertiesisavailable
ANGLESSubroutine
"angles" finds the total number of bond angles and stores the atom numbers of the atoms defining
eachangle;foreachangletoatrivalentcentralatom,thethirdbondedatomisstoredforuseinoutof-planebending
ANNEALProgram
"anneal" performs a simulated annealing protocol by means of variable temperature molecular
dynamicsusingeitherlinear,exponentialorsigmoidalcoolingschedules
ANORMFunction
"anorm"findsthenorm(length)ofavector;usedasaserviceroutinebytheConnollysurfacearea
andvolumecomputation
ARCHIVEProgram
"archive"isautilityprogramforcoordinatefileswhichconcatenatesmultiplecoordinatesetsintoa
singlearchivefile,orextractsindividualcoordinatesetsfromanarchive
ASETSubroutine
"aset" computes by recursion the A functions used in the evaluation of Slater-type (STO) overlap
integrals
ATOMYZESubroutine
"atomyze"printsthepotentialenergycomponentsbrokendownbyatomandtoachoiceofprecision
ATTACHSubroutine
"attach"generateslistsof1-3,1-4and1-5connectivitiesstartingfromthepreviouslydeterminedlist
ofattachedatoms(ie,1-2connectivity)
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BASEFILESubroutine
"basefile"extractsfromaninputfilenametheportionconsistingofanydirectorynameandthebase
filename
BCUCOFSubroutine
"bcucof" determines the coefficient matrix needed for bicubic interpolation of a function, gradients
andcrossderivatives
BCUINTSubroutine
"bcuint"performsabicubicinterpolationofthefunctionvalueona2Dsplinegrid
BCUINT1Subroutine
"bcuint1"performsabicubicinterpolationofthefunctionvalueandgradientalongthedirectionsofa
2Dsplinegrid
BCUINT2Subroutine
"bcuint2" performs a bicubic interpolation of the function value, gradient and Hessain along the
directionsofa2Dsplinegrid
BEEMANSubroutine
"beeman"performsasinglemoleculardynamicstimestepbymeansofaBeemanmultisteprecursion
formula;theactualcoefficientsareBrooks'"BetterBeeman"values
BETACFFunction
"betacf"computesarapidlyconvergentcontinuedfractionneededbyroutine"betai"toevaluatethe
cumulativeBetadistribution
BETAIFunction
"betai"evaluatesthecumulativeBetadistributionfunctionastheprobabilitythatarandomvariable
fromadistributionwithBetaparameters"a"and"b"willbelessthan"x"
BIGBLOCKSubroutine
"bigblock"replicatesthecoordinatesofasingleunitcelltogivealargerblockofrepeatedunits
BITORSSubroutine
"bitors"findsthetotalnumberofbitorsions,pairsofoverlappingdihedralangles,andthenumbersof
thefiveatomsdefiningeachbitorsion
BMAXFunction
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"bmax"computesthemaximumorderoftheBfunctionsneededforevaluationofSlater-type(STO)
overlapintegrals
BNDERRFunction
"bnderr"isthedistancebounderrorfunctionandderivatives;thisversionimplementstheoriginal
and Havel's normalized lower bound penalty, the normalized version is preferred when lower
boundsaresmall(aswithNMRNOErestraints),theoriginalpenaltyisneedediflargelowerbounds
arepresent
BONDSSubroutine
"bonds"findsthetotalnumberofcovalentbondsandstorestheatomnumbersoftheatomsdefining
eachbond
BORNSubroutine
"born"computestheBornradiusofeachatomforusewiththevariousGB/SAsolvationmodels
BORN1Subroutine
"born1" computes derivatives of the Born radii with respect to atomic coordinates and increments
totalenergyderivativesandvirialcomponentsforpotentialsinvolvingBornradii
BOUNDSSubroutine
"bounds"findsthecenterofmassofeachmoleculeandtranslatesanystraymoleculesbackintothe
periodicbox
BSETSubroutine
"bset"computesbydownwardrecursiontheBfunctionsusedintheevaluationofSlater-type(STO)
overlapintegrals
BSPLINESubroutine
"bspline"calculatesthecoefficientsforann-thorderB-splineapproximation
BSPLINE1Subroutine
"bspline1" calculates the coefficients and derivative coefficients for an n-th order B-spline
approximation
BSSTEPSubroutine
"bsstep" takes a single Bulirsch-Stoer step with monitoring of local truncation error to ensure
accuracy
CALENDARSubroutine
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"calendar"returnsthecurrenttimeasasetofintegervaluesrepresentingtheyear,month,day,hour,
minuteandsecond
CELLATOMSubroutine
"cellatom" completes the addition of a symmetry related atom to a unit cell by updating the atom
typeandattachmentarrays
CENTERSubroutine
"center" moves the weighted centroid of each coordinate set to the origin during least squares
superposition
CERRORSubroutine
"cerror"istheerrorhandlingroutinefortheConnollysurfaceareaandvolumecomputation
CFFTBSubroutine
"cfftb"computesthebackwardcomplexdiscreteFouriertransform,theFouriersynthesis
CFFTB1Subroutine
CFFTFSubroutine
"cfftf"computestheforwardcomplexdiscreteFouriertransform,theFourieranalysis
CFFTF1Subroutine
CFFTISubroutine
"cffti" initializes the array "wsave" which is used in both forward and backward transforms; the
primefactorizationof"n"togetherwithatabulationofthetrigonometricfunctionsarecomputedand
storedin"wsave"
CFFTI1Subroutine
CHIRERFunction
"chirer"computesthechiralityerroranditsderivativeswithrespecttoatomicCartesiancoordinates
asasumthesquaresofdeviationsofchiralvolumesfromtargetvalues
CHKCLASHSubroutine
"chkclash"determinesifthereareanyatomclasheswhichmightcausetroubleonsubsequentenergy
evaluation
CHKPOLESubroutine
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"chkpole"invertsatomicmultipolemomentsasnecessaryatsiteswithchirallocalreferenceframe
definitions
CHKRINGSubroutine
"chkring" tests angles to be constrained for their presence in small rings and removes constraints
thatareredundant
CHKSIZESubroutine
"chksize"computesameasureofoverallglobalstructuralexpansionorcompactionfromthenumber
ofexcessupperorlowerboundsmatrixviolations
CHKTREESubroutine
"chktree" tests a minimum energy structure to see if it belongs to the correct progenitor in the
existingmap
CHKXYZSubroutine
"chkxyz"findsanypairsofatomswithidenticalCartesiancoordinates,andprintsawarningmessage
CHOLESKYSubroutine
"cholesky"usesamodifiedCholeskymethodtosolvethelinearsystemAx=b,returning"x"in"b";
"A"isassumedtobearealsymmetricpositivedefinitematrixwithitsdiagonalanduppertriangle
storedbyrows
CIRPLNSubroutine
CJKMFunction
"cjkm"computesthecoefficientsofsphericalharmonicsexpressedinprolatespheroidalcoordinates
CLIMBERSubroutine
CLIMBRGDSubroutine
CLIMBROTSubroutine
CLIMBTORSubroutine
CLIMBXYZSubroutine
CLOCKSubroutine
"clock"determineselapsedCPUtimeinsecondssincethestartofthejob
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CLUSTERSubroutine
"cluster"getsthepartitioningofthesystemintogroupsandstoresalistofthegrouptowhicheach
atombelongs
COLUMNSubroutine
"column"takestheoff-diagonalHessianelementsstoredassparserowsandsetsupindicestoallow
columnaccess
COMMANDSubroutine
"command" uses the standard Unix-like iargc/getarg routines to get the number and values of
argumentsspecifiedonthecommandlineatprogramruntime
COMPRESSSubroutine
"compress"transfersonlythenon-buriedtorifromthetemporarytoriarraystothefinaltoriarrays
CONNECTSubroutine
"connect"setsuptheattachedatomarraysstartingfromasetofinternalcoordinates
CONNOLLYSubroutine
"connolly" uses the algorithms from the AMS/VAM programs of Michael Connolly to compute the
analyticalmolecularsurfaceareaandvolumeofacollectionofsphericalatoms;thusitimplements
Fred Richards' molecular surface definition as a set of analytically defined spherical and toroidal
polygons
CONTACTSubroutine
"contact"constructsthecontactsurface,cyclesandconvexfaces
CONTROLSubroutine
"control" gets initial values for parameters that determine the output style and information level
providedbyTINKER
COORDSSubroutine
"coords" converts the three principal eigenvalues/vectors from the metric matrix into atomic
coordinates,andcallsaroutinetocomputethermsdeviationfromthebounds
CORRELATEProgram
"correlate" computes the time correlation function of some user-supplied property from individual
snapshotframestakenfromamoleculardynamicsorothertrajectory
CREATEJVMSubroutine
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CREATESERVERSubroutine
CREATESYSTEMSubroutine
CREATEUPDATESubroutine
CRYSTALProgram
"crystal"isautilityprogramwhichconvertsbetweenfractionalandCartesiancoordinates,andcan
generatefullunitcellsfromasymmetricunits
CUTOFFSSubroutine
"cutoffs"initializesandstoressphericalenergycutoffdistancewindows,HessianelementandEwald
sumcutoffs,andthepairwiseneighborgenerationmethod
CYTSYSubroutine
"cytsy" solves a system of linear equations for a cyclically tridiagonal, symmetric, positive definite
matrix
CYTSYPSubroutine
"cytsyp" finds the Cholesky factors of a cyclically tridiagonal symmetric, positive definite matrix
givenbytwovectors
CYTSYSSubroutine
"cytsys"solvesacyclicallytridiagonallinearsystemgiventheCholeskyfactors
D1D2Function
"d1d2"isautilityfunctionusedincomputationofthereactionfieldrecursivesummationelements
DELETESubroutine
"delete"removesaspecifiedatomfromtheCartesiancoordinateslistandshiftstheremainingatoms
DEPTHFunction
DESTROYJVMSubroutine
DESTROYSERVERSubroutine
DFTMODSubroutine
"dftmod" computes the modulus of the discrete Fourier transform of "bsarray", storing it into
"bsmod"
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DIAGQSubroutine
"diagq" is a matrix diagonalization routine which is derived from the classical given, housec, and
eigenalgorithmswithseveralmodificationstoincreasetheefficiencyandaccuracy
DIFFEQSubroutine
"diffeq" performs the numerical integration of an ordinary differential equation using an adaptive
stepsizemethodtosolvethecorrespondingcoupledfirst-orderequationsofthegeneralformdyi/dx
=f(x,y1,...,yn)foryi=y1,...,yn
DIFFUSEProgram
"diffuse" finds the self-diffusion constant for a homogeneous liquid via the Einstein relation from a
setofstoredmoleculardynamicsframes;molecularcentersofmassareunfoldedandmeansquared
displacementsarecomputedversustimeseparation
DIST2Function
"dist2" finds the distance squared between two points; used as a service routine by the Connolly
surfaceareaandvolumecomputation
DISTGEOMProgram
"distgeom"usesametricmatrixdistancegeometryproceduretogeneratestructureswithinterpoint
distances that lie within specified bounds, with chiral centers that maintain chirality, and with
torsionalanglesrestrainedtodesiredvalues;theuseralsohastheabilitytointeractivelyinspectand
alterthetrianglesmoothedboundsmatrixpriortoembedding
DMDUMPSubroutine
"dmdump"putsthedistancematrixofthefinalstructureintotheupperhalfofamatrix,thedistance
ofeachatomtothecentroidonthediagonal,andtheindividualtermsoftheboundserrorsintothe
lowerhalfofthematrix
DOCUMENTProgram
"document"generatesaformatteddescriptionofallthecodemodulesorcommonblocks,anindexof
routines called by each source code module, a listing of all valid keywords, a list of include file
dependenciesasneededbyaUnix-styleMakefile,oraformattedforcefieldparametersetsummary
DOTFunction
"dot"findsthedotproductoftwovectors
DSTMATSubroutine
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"dstmat" selects a distance matrix containing values between the previously smoothed upper and
lower bounds; the distance values are chosen from uniform distributions, in a triangle correlated
fashion,orusingrandompartialmetrization
DYNAMICProgram
"dynamic" computes a molecular dynamics trajectory in any of several statistical mechanical
ensembles with optional periodic boundaries and optional coupling to temperature and pressure
bathsalternativelyastochasticdynamicstrajectorycanbegenerated
EANGANGSubroutine
"eangang"calculatestheangle-anglepotentialenergy
EANGANG1Subroutine
"eangang1"calculatestheangle-anglepotentialenergyandfirstderivativeswithrespecttoCartesian
coordinates
EANGANG2Subroutine
"eangang2"calculatestheangle-anglepotentialenergysecondderivativeswithrespecttoCartesian
coordinatesusingfinitedifferencemethods
EANGANG2ASubroutine
"eangang2a" calculates the angle-angle first derivatives for a single interaction with respect to
Cartesiancoordinates;usedincomputationoffinitedifferencesecondderivatives
EANGANG3Subroutine
"eangang3"calculatestheangle-anglepotentialenergy;alsopartitionstheenergyamongtheatoms
EANGLESubroutine
"eangle"calculatestheanglebendingpotentialenergy;projectedin-planeanglesattrigonalcenters
orFourieranglebendingtermsareoptionallyused
EANGLE1Subroutine
"eangle1" calculates the angle bending potential energy and the first derivatives with respect to
Cartesiancoordinates;projectedin-planeanglesattrigonalcentersorFourieranglebendingterms
areoptionallyused
EANGLE2Subroutine
"eangle2"calculatessecondderivativesoftheanglebendingenergyforasingleatomusingamixture
of analytical and finite difference methods; projected in-plane angles at trigonal centers or Fourier
anglebendingtermsareoptionallyused
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EANGLE2ASubroutine
"eangle2a" calculates bond angle bending potential energy second derivatives with respect to
Cartesiancoordinates
EANGLE2BSubroutine
"eangle2b" computes projected in-plane bending first derivatives for a single angle with respect to
Cartesiancoordinates;usedincomputationoffinitedifferencesecondderivatives
EANGLE3Subroutine
"eangle3"calculatestheanglebendingpotentialenergy,alsopartitionstheenergyamongtheatoms;
projectedin-planeanglesattrigonalcentersorFourieranglebendingtermsareoptionallyused
EBONDSubroutine
"ebond"calculatesthebondstretchingenergy
EBOND1Subroutine
"ebond1" calculates the bond stretching energy and first derivatives with respect to Cartesian
coordinates
EBOND2Subroutine
"ebond2"calculatessecondderivativesofthebondstretchingenergyforasingleatomatatime
EBOND3Subroutine
"ebond3"calculatesthebondstretchingenergy;alsopartitionstheenergyamongtheatoms
EBUCKSubroutine
"ebuck"calculatestheBuckinghamexp-6vanderWaalsenergy
EBUCK0ASubroutine
"ebuck0a"calculatestheBuckinghamexp-6vanderWaalsenergyusingapairwisedoubleloop
EBUCK0BSubroutine
"ebuck0b" calculates the Buckingham exp-6 van der Waals energy using the method of lights to
locateneighboringatoms
EBUCK0CSubroutine
"ebuck0c"calculatestheBuckinghamexp-6vanderWaalsenergyviaaGaussianapproximationfor
potentialenergysmoothing
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EBUCK1Subroutine
"ebuck1"calculatestheBuckinghamexp-6vanderWaalsenergyanditsfirstderivativeswithrespect
toCartesiancoordinates
EBUCK1ASubroutine
"ebuck1a" calculates the Buckingham exp-6 van der Waals energy and its first derivatives using a
pairwisedoubleloop
EBUCK1BSubroutine
"ebuck1b"calculatestheBuckinghamexp-6vanderWaalsenergyanditsfirstderivativesusingthe
methodoflightstolocateneighboringatoms
EBUCK1CSubroutine
"ebuck1c" calculates the Buckingham exp-6 van der Waals energy and its first derivatives via a
Gaussianapproximationforpotentialenergysmoothing
EBUCK2Subroutine
"ebuck2" calculates the Buckingham exp-6 van der Waals second derivatives for a single atom at a
time
EBUCK2ASubroutine
"ebuck2a" calculates the Buckingham exp-6 van der Waals second derivatives using a double loop
overrelevantatompairs
EBUCK2BSubroutine
"ebuck2b" calculates the Buckingham exp-6 van der Waals second derivatives via a Gaussian
approximationforusewithpotentialenergysmoothing
EBUCK3Subroutine
"ebuck3" calculates the Buckingham exp-6 van der Waals energy and partitions the energy among
theatoms
EBUCK3ASubroutine
"ebuck3a"calculatestheBuckinghamexp-6vanderWaalsenergyandpartitionstheenergyamong
theatomsusingapairwisedoubleloop
EBUCK3BSubroutine
"ebuck3b" calculates the Buckingham exp-6 van der Waals energy and also partitions the energy
amongtheatomsusingthemethodoflightstolocateneighboringatoms
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EBUCK3CSubroutine
"ebuck3c"calculatestheBuckinghamexp-6vanderWaalsenergyviaaGaussianapproximationfor
potentialenergysmoothing
ECHARGESubroutine
"echarge"calculatesthecharge-chargeinteractionenergy
ECHARGE0ASubroutine
"echarge0a"calculatesthecharge-chargeinteractionenergyusingapairwisedoubleloop
ECHARGE0BSubroutine
"echarge0b" calculates the charge-charge interaction energy using the method of lights to locate
neighboringatoms
ECHARGE0CSubroutine
"echarge0c" calculates the charge-charge interaction energy for use with potential smoothing
methods
ECHARGE0DSubroutine
"echarge0d"calculatesthecharge-chargeinteractionenergyusingaparticlemeshEwaldsummation
ECHARGE0ESubroutine
"echarge0e"calculatesthecharge-chargeinteractionenergyusingaparticlemeshEwaldsummation
andthemethodoflightstolocateneighboringatoms
ECHARGE1Subroutine
"echarge1" calculates the charge-charge interaction energy and first derivatives with respect to
Cartesiancoordinates
ECHARGE1ASubroutine
"echarge1a" calculates the charge-charge interaction energy and first derivatives with respect to
Cartesiancoordinatesusingapairwisedoubleloop
ECHARGE1BSubroutine
"echarge1b" calculates the charge-charge interaction energy and first derivatives with respect to
Cartesiancoordinatesusingthemethodoflightstolocateneighboringatoms
ECHARGE1CSubroutine
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"echarge1c" calculates the charge-charge interaction energy and first derivatives with respect to
Cartesiancoordinatesforusewithpotentialsmoothingmethods
ECHARGE1DSubroutine
"echarge1d" calculates the charge-charge interaction energy and first derivatives with respect to
CartesiancoordinatesusingaparticlemeshEwaldsummation
ECHARGE2Subroutine
"echarge2"calculatessecondderivativesofthecharge-chargeinteractionenergyforasingleatom
ECHARGE2ASubroutine
"echarge2a"calculatessecondderivativesofthecharge-chargeinteractionenergyforasingleatom
usingapairwisedoubleloop
ECHARGE2BSubroutine
"echarge2b"calculatessecondderivativesofthecharge-chargeinteractionenergyforasingleatom
forusewithpotentialsmoothingmethods
ECHARGE2CSubroutine
"echarge2c"calculatessecondderivativesofthecharge-chargeinteractionenergyforasingleatom
usingaparticlemeshEwaldsummation
ECHARGE3Subroutine
"echarge3" calculates the charge-charge interaction energy and partitions the energy among the
atoms
ECHARGE3ASubroutine
"echarge3a" calculates the charge-charge interaction energy and partitions the energy among the
atomsusingapairwisedoubleloop
ECHARGE3BSubroutine
"echarge3b" calculates the charge-charge interaction energy and partitions the energy among the
atomsusingthemethodoflightstolocateneighboringatoms
ECHARGE3CSubroutine
"echarge3c" calculates the charge-charge interaction energy and partitions the energy among the
atomsforusewithpotentialsmoothingmethods
ECHARGE3DSubroutine
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"echarge3d" calculates the charge-charge interaction energy and partitions the energy among the
atomsusingaparticlemeshEwaldsummation
ECHARGE3ESubroutine
"echarge3e" calculates the charge-charge interaction energy and partitions the energy among the
atomsusingaparticlemeshEwaldsummationandthemethodoflightstolocateneighboringatoms
ECHGDPLSubroutine
"echgdpl"calculatesthecharge-dipoleinteractionenergy
ECHGDPL1Subroutine
"echgdpl1" calculates the charge-dipole interaction energy and first derivatives with respect to
Cartesiancoordinates
ECHGDPL2Subroutine
"echgdpl2"calculatessecondderivativesofthecharge-dipoleinteractionenergyforasingleatom
ECHGDPL3Subroutine
"echgdpl3" calculates the charge-dipole interaction energy; also partitions the energy among the
atoms
EDIPOLESubroutine
"edipole"calculatesthedipole-dipoleinteractionenergy
EDIPOLE1Subroutine
"edipole1" calculates the dipole-dipole interaction energy and first derivatives with respect to
Cartesiancoordinates
EDIPOLE2Subroutine
"edipole2"calculatessecondderivativesofthedipole-dipoleinteractionenergyforasingleatom
EDIPOLE3Subroutine
"edipole3" calculates the dipole-dipole interaction energy; also partitions the energy among the
atoms
EGAUSSSubroutine
"egauss"calculatestheGaussianexpansionvanderWaalsinteractionenergy
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EGAUSS0ASubroutine
"egauss0a" calculates the Gaussian expansion van der Waals interaction energy using a pairwise
doubleloop
EGAUSS0BSubroutine
"egauss0b"calculatestheGaussianexpansionvanderWaalsinteractionenergyforusewithpotential
energysmoothing
EGAUSS1Subroutine
"egauss1" calculates the Gaussian expansion van der Waals interaction energy and its first
derivativeswithrespecttoCartesiancoordinates
EGAUSS1ASubroutine
"egauss1a" calculates the Gaussian expansion van der Waals interaction energy and its first
derivativesusingapairwisedoubleloop
EGAUSS1BSubroutine
"egauss1b" calculates the Gaussian expansion van der Waals interaction energy and its first
derivativesforusewithstophatpotentialenergysmoothing
EGAUSS2Subroutine
"egauss2"calculatestheGaussianexpansionvanderWaalssecondderivativesforasingleatomata
time
EGAUSS2ASubroutine
"egauss2a" calculates the Gaussian expansion van der Waals second derivatives using a pairwise
doubleloop
EGAUSS2BSubroutine
"egauss2b"calculatestheGaussianexpansionvanderWaalssecondderivativesforstophatpotential
energysmoothing
EGAUSS3Subroutine
"egauss3" calculates the Gaussian expansion van der Waals interaction energy and partitions the
energyamongtheatoms
EGAUSS3ASubroutine
"egauss3a" calculates the Gaussian expansion van der Waals interaction energy and partitions the
energyamongtheatomsusingapairwisedoubleloop
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EGAUSS3BSubroutine
"egauss3b" calculates the Gaussian expansion van der Waals interaction energy and partitions the
energyamongtheatomsusingapairwisedoubleloop
EGBSA0ASubroutine
"egbsa0a"calculatesthegeneralizedBornpolarizationenergyfortheGB/SAsolvationmodels
EGBSA0BSubroutine
"egbsa0b" calculates the generalized Born polarization energy for the GB/SA solvation models for
usewithpotentialsmoothingmethodsviaanalogytothesmoothingofCoulomb'slaw
EGBSA1ASubroutine
"egbsa1a"calculatesthegeneralizedBornenergyandfirstderivativesoftheGB/SAsolvationmodels
EGBSA1BSubroutine
"egbsa1b"calculatesthegeneralizedBornenergyandfirstderivativesoftheGB/SAsolvationmodels
forusewithpotentialsmoothingmethods
EGBSA2ASubroutine
"egbsa2a"calculatessecondderivativesofthegeneralizedBornenergytermfortheGB/SAsolvation
models
EGBSA2BSubroutine
"egbsa2b"calculatessecondderivativesofthegeneralizedBornenergytermfortheGB/SAsolvation
modelsforusewithpotentialsmoothingmethods
EGBSA3ASubroutine
"egbsa3a" calculates the generalized Born energy term for the GB/SA solvation models; also
partitionstheenergyamongtheatoms
EGBSA3BSubroutine
"egbsa3b" calculates the generalized Born polarization energy for the GB/SA solvation models for
usewithpotentialsmoothingmethodsviaanalogytothesmoothingofCoulomb'slaw;alsopartitions
theenergyamongtheatoms
EGEOMSubroutine
"egeom"calculatestheenergyduetorestraintsonpositions,distances,anglesandtorsionsaswellas
Gaussianbasinandsphericaldropletrestraints
EGEOM1Subroutine
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"egeom1" calculates the energy and first derivatives with respect to Cartesian coordinates due to
restraintsonpositions,distances,anglesandtorsionsaswellasGaussianbasinandsphericaldroplet
restraints
EGEOM2Subroutine
"egeom2" calculates second derivatives of restraints on positions, distances, angles and torsions as
wellasGaussianbasinandsphericaldropletrestraints
EGEOM3Subroutine
"egeom3"calculatestheenergyduetorestraintsonpositions,distances,anglesandtorsionsaswell
asGaussianbasinanddropletrestraints;alsopartitionsenergyamongtheatoms
EHALSubroutine
"ehal"calculatesthebuffered14-7vanderWaalsenergy
EHAL0ASubroutine
"ehal0a"calculatesthebuffered14-7vanderWaalsenergyusingapairwisedoubleloop
EHAL0BSubroutine
"ehal0a" calculates the buffered 14-7 van der Waals energy using the method of lights to locate
neighboringatoms
EHAL1Subroutine
"ehal1" calculates the buffered 14-7 van der Waals energy and its first derivatives with respect to
Cartesiancoordinates
EHAL1ASubroutine
"ehal1a"calculatesthebuffered14-7vanderWaalsenergyanditsfirstderivativeswithrespectto
Cartesiancoordinatesusingapairwisedoubleloop
EHAL1BSubroutine
"ehal1b"calculatesthebuffered14-7vanderWaalsenergyanditsfirstderivativeswithrespectto
Cartesiancoordinatesusingthemethodoflightstolocateneighboringatoms
EHAL2Subroutine
"ehal2"calculatesthebuffered14-7vanderWaalssecondderivativesforasingleatomatatime
EHAL3Subroutine
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"ehal3" calculates the buffered 14-7 van der Waals energy and partitions the energy among the
atoms
EHAL3ASubroutine
"ehal3a" calculates the buffered 14-7 van der Waals energy and partitions the energy among the
atomsusingapairwisedoubleloop
EHAL3BSubroutine
"ehal3b"calculatesthebuffered14-7vanderWaalsenergyandalsopartitionstheenergyamongthe
atomsusingthemethodoflightstolocateneighboringatoms
EIGENSubroutine
"eigen" uses the power method to compute the largest eigenvalues and eigenvectors of the metric
matrix,"valid"issettrueifthefirstthreeeigenvaluesarepositive
EIGENRGDSubroutine
EIGENROTSubroutine
EIGENROTSubroutine
EIGENTORSubroutine
EIGENXYZSubroutine
EIMPROPSubroutine
"eimprop"calculatestheimproperdihedralpotentialenergy
EIMPROP1Subroutine
"eimprop1" calculates improper dihedral energy and its first derivatives with respect to Cartesian
coordinates
EIMPROP2Subroutine
"eimprop2"calculatessecondderivativesoftheimproperdihedralangleenergyforasingleatom
EIMPROP3Subroutine
"eimprop3" calculates the improper dihedral potential energy; also partitions the energy terms
amongtheatoms
EIMPTORSubroutine
"eimptor"calculatestheimpropertorsionpotentialenergy
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EIMPTOR1Subroutine
"eimptor1" calculates improper torsion energy and its first derivatives with respect to Cartesian
coordinates
EIMPTOR2Subroutine
"eimptor2"calculatessecondderivativesoftheimpropertorsionenergyforasingleatom
EIMPTOR3Subroutine
"eimptor3"calculatestheimpropertorsionpotentialenergy;alsopartitionstheenergytermsamong
theatoms
ELJSubroutine
"elj"calculatestheLennard-Jones6-12vanderWaalsenergy
ELJ0ASubroutine
"elj0a"calculatestheLennard-Jones6-12vanderWaalsenergyusingapairwisedoubleloop
ELJ0BSubroutine
"elj0b"calculatestheLennard-Jones6-12vanderWaalsenergyusingthemethodoflightstolocate
neighboringatoms
ELJ0CSubroutine
"elj0c" calculates the Lennard-Jones 6-12 van der Waals energy via a Gaussian approximation for
potentialenergysmoothing
ELJ0DSubroutine
"elj0d"calculatestheLennard-Jones6-12vanderWaalsenergyforusewithstophatpotentialenergy
smoothing
ELJ1Subroutine
"elj1"calculatestheLennard-Jones6-12vanderWaalsenergyanditsfirstderivativeswithrespectto
Cartesiancoordinates
ELJ1ASubroutine
"elj1a" calculates the Lennard-Jones 6-12 van der Waals energy and its first derivatives using a
pairwisedoubleloop
ELJ1BSubroutine
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"elj1b" calculates the Lennard-Jones 6-12 van der Waals energy and its first derivatives using the
methodoflightstolocateneighboringatoms
ELJ1CSubroutine
"elj1c" calculates the Lennard-Jones 6-12 van der Waals energy and its first derivatives via a
Gaussianapproximationforpotentialenergysmoothing
ELJ1DSubroutine
"elj1d"calculatesthevanderWaalsinteractionenergyanditsfirstderivativesforusewithstophat
potentialenergysmoothing
ELJ2Subroutine
"elj2"calculatestheLennard-Jones6-12vanderWaalssecondderivativesforasingleatomatatime
ELJ2ASubroutine
"elj2a"calculatestheLennard-Jones6-12vanderWaalssecondderivativesusingadoubleloopover
relevantatompairs
ELJ2BSubroutine
"elj2b" calculates the Lennard-Jones 6-12 van der Waals second derivatives via a Gaussian
approximationforusewithpotentialenergysmoothing
ELJ2CSubroutine
"elj2c" calculates the Lennard-Jones 6-12 van der Waals second derivatives for use with stophat
potentialenergysmoothing
ELJ3Subroutine
"elj3"calculatestheLennard-Jones6-12vanderWaalsenergyandalsopartitionstheenergyamong
theatoms
ELJ3ASubroutine
"elj3a"calculatestheLennard-Jones6-12vanderWaalsenergyandalsopartitionstheenergyamong
theatomsusingapairwisedoubleloop
ELJ3BSubroutine
"elj3b"calculatestheLennard-Jones6-12vanderWaalsenergyandalsopartitionstheenergyamong
theatomsusingthemethodoflightstolocateneighboringatoms
ELJ3CSubroutine
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"elj3c"calculatestheLennard-Jones6-12vanderWaalsenergyandalsopartitionstheenergyamong
theatomsviaaGaussianapproximationforpotentialenergysmoothing
ELJ3DSubroutine
"elj3d"calculatestheLennard-Jones6-12vanderWaalsenergyandalsopartitionstheenergyamong
theatomsforusewithstophatpotentialenergysmoothing
EMBEDSubroutine
"embed"isadistancegeometryroutinepatternedaftertheideasofGordonCrippen,IrwinKuntzand
Tim Havel; it takes as input a set of upper and lower bounds on the interpoint distances, chirality
restraintsandtorsionalrestraints,andattemptstogenerateasetofcoordinatesthatsatisfytheinput
boundsandrestraints
EMETALSubroutine
"emetal"calculatesthetransitionmetalligandfieldenergy
EMETAL1Subroutine
"emetal1"calculatesthetransitionmetalligandfieldenergyanditsfirstderivativeswithrespectto
Cartesiancoordinates
EMETAL2Subroutine
"emetal2"calculatesthetransitionmetalligandfieldsecondderivativesforasingleatomatatime
EMETAL3Subroutine
"emetal3"calculatesthetransitionmetalligandfieldenergyandalsopartitionstheenergyamongthe
atoms
EMM3HBSubroutine
"emm3hb" calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen
bondingenergy
EMM3HB0ASubroutine
"emm3hb0a" calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen
bondingenergyusingapairwisedoubleloop
EMM3HB0BSubroutine
"emm3hb0b" calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen
bondingenergyusingthemethodoflightstolocateneighboringatoms
EMM3HB1Subroutine
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"emm3hb1" calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen
bondingenergywithrespecttoCartesiancoordinates
EMM3HB1ASubroutine
"emm3hb1a" calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen
bondingenergywithrespecttoCartesiancoordinatesusingapairwisedoubleloop
EMM3HB1BSubroutine
"emm3hb1b" calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen
bonding energy with respect to Cartesian coordinates using the method of lights to locate
neighboringatoms
EMM3HB2Subroutine
"emm3hb2" calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen
bondingsecondderivativesforasingleatomatatime
EMM3HB3Subroutine
"emm3hb3" calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen
bondingenergy,andpartitionstheenergyamongtheatoms
EMM3HB3ASubroutine
"emm3hb3" calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen
bondingenergy,andpartitionstheenergyamongtheatoms
EMM3HB3BSubroutine
"emm3hb3b" calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen
bondingenergyusingthemethodoflightstolocateneighboringatoms
EMPOLESubroutine
"empole" calculates the electrostatic energy due to atomic multipole interactions and dipole
polarizability
EMPOLE0ASubroutine
"empole0a" calculates the electrostatic energy due to atomic multipole interactions and dipole
polarizabilityusingapairwisedoubleloop
EMPOLE0BSubroutine
"empole0b" calculates the electrostatic energy due to atomic multipole interactions and dipole
polarizabilityusingaregularEwaldsummation
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EMPOLE1Subroutine
"empole1" calculates the multipole and dipole polarization energy and derivatives with respect to
Cartesiancoordinates
EMPOLE1ASubroutine
"empole1a"calculatesthemultipoleanddipolepolarizationenergyandderivativeswithrespectto
Cartesiancoordinatesusingapairwisedoubleloop
EMPOLE1BSubroutine
"empole1b"calculatesthemultipoleanddipolepolarizationenergyandderivativeswithrespectto
CartesiancoordinatesusingaregularEwaldsummation
EMPOLE2Subroutine
"empole2"calculatessecondderivativesofthemultipoleanddipolepolarizationenergyforasingle
atomatatime
EMPOLE2ASubroutine
"empole2a" computes multipole and dipole polarization first derivatives for a single atom with
respecttoCartesiancoordinates;usedtogetfinitedifferencesecondderivatives
EMPOLE3Subroutine
"empole3" calculates the electrostatic energy due to atomic multipole interactions and dipole
polarizability,andpartitionstheenergyamongtheatoms
EMPOLE3ASubroutine
"empole3a" calculates the electrostatic energy due to atomic multipole interactions and dipole
polarizability,andpartitionstheenergyamongtheatomsusingadoubleloop
EMPOLE3BSubroutine
"empole3b" calculates the electrostatic energy due to atomic multipole interactions and dipole
polarizability,andpartitionstheenergyamongtheatomsusingaregularEwaldsummation
ENERGYFunction
"energy"callsthesubroutinestocalculatethepotentialenergytermsandsumsuptoformthetotal
energy
ENRGYZESubroutine
"energyze" is an auxiliary routine for the analyze program that performs the energy analysis and
printsthetotalandintermolecularenergies
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EOPBENDSubroutine
"eopbend"computestheout-of-planebendpotentialenergyattrigonalcentersviaaWilson-DeciusCrossanglebend
EOPBEND1Subroutine
"eopbend1"computestheout-of-planebendpotentialenergyandfirstderivativesattrigonalcenters
viaaWilson-Decius-Crossanglebend
EOPBEND2Subroutine
"eopbend2"calculatessecondderivativesoftheout-of-planebendenergyviaaWilson-Decius-Cross
anglebendforasingleatomusingfinitedifferencemethods
EOPBEND2ASubroutine
"eopbend2a" calculates out-of-plane bending first derivatives at a trigonal center via a WilsonDecius-Crossanglebend;usedincomputationoffinitedifferencesecondderivatives
EOPBEND3Subroutine
"eopbend3"computestheout-of-planebendpotentialenergyattrigonalcentersviaaWilson-DeciusCrossanglebend;alsopartitionstheenergyamongtheatoms
EOPDISTSubroutine
"eopdist" computes the out-of-plane distance potential energy at trigonal centers via the central
atomheight
EOPDIST1Subroutine
"eopdist1" computes the out-of-plane distance potential energy and first derivatives at trigonal
centersviathecentralatomheight
EOPDIST2Subroutine
"eopdist2"calculatessecondderivativesoftheout-of-planedistanceenergyforasingleatomviathe
centralatomheight
EOPDIST3Subroutine
"eopdist3" computes the out-of-plane distance potential energy at trigonal centers via the central
atomheight;alsopartitionstheenergyamongtheatoms
EPITORSSubroutine
"epitors"calculatesthepi-orbitaltorsionpotentialenergy
EPITORS1Subroutine
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"epitors1" calculates the pi-orbital torsion potential energy and first derivatives with respect to
Cartesiancoordinates
EPITORS2Subroutine
"epitors2" calculates the second derivatives of the pi-orbital torsion energy for a single atom using
finitedifferencemethods
EPITORS2ASubroutine
"epitors2a"calculatesthepi-orbitaltorsionfirstderivatives;usedincomputationoffinitedifference
secondderivatives
EPITORS3Subroutine
"epitors3"calculatesthepi-orbitaltorsionpotentialenergy;alsopartitionstheenergytermsamong
theatoms
EPMESubroutine
"epme" computes the reciprocal space energy for a particle mesh Ewald summation over partial
charges
EPME1Subroutine
"epme1" computes the reciprocal space energy and first derivatives for a particle mesh Ewald
summation
EPME3Subroutine
"epme3" computes the reciprocal space energy for a particle mesh Ewald summation over partial
chargesandprintsinformationabouttheenergyoverthechargegridpoints
EPUCLCSubroutine
EREALSubroutine
"ereal" evaluates the real space portion of the regular Ewald summation energy due to atomic
multipoleinteractionsanddipolepolarizability
EREAL1Subroutine
"ereal1"evaluatestherealspaceportionoftheregularEwaldsummationenergyandgradientdueto
atomicmultipoleinteractionsanddipolepolarizability
EREAL3Subroutine
"ereal3" evaluates the real space portion of the regular Ewald summation energy due to atomic
multipoleinteractionsanddipolepolarizabilityandpartitionstheenergyamongtheatoms
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ERECIPSubroutine
"erecip"evaluatesthereciprocalspaceportionoftheregularEwaldsummationenergyduetoatomic
multipoleinteractionsanddipolepolarizability
ERECIP1Subroutine
"erecip1" evaluates the reciprocal space portion of the regular Ewald summation energy and
gradientduetoatomicmultipoleinteractionsanddipolepolarizability
ERECIP3Subroutine
"erecip3" evaluates the reciprocal space portion of the regular Ewald summation energy due to
atomicmultipoleinteractionsanddipolepolarizability,andprintsinformationabouttheenergyover
thereciprocallatticevectors
ERFFunction
"erf" computes a numerical approximation to the value of the error function via a Chebyshev
approximation
ERFCFunction
"erfc"computesanumericalapproximationtothevalueofthecomplementaryerrorfunctionviaa
Chebyshevapproximation
ERFCORESubroutine
"erfcore"evaluateserf(x)orerfc(x)forarealargumentx;whencalledwithmodesetto0itreturns
erf,amodeof1returnserfc;usesrationalfunctionsthatapproximateerf(x)anderfc(x)toatleast18
significantdecimaldigits
ERFIKSubroutine
"erfik"computethereactionfieldenergyduetoasinglepairofatomicmultipoles
ERFINVFunction
"erfinv"evaluatestheinverseoftheerrorfunctionerfforarealargumentintherange(-1,1)usinga
rationalfunctionapproximationfollowedbycyclesofNewton-Raphsoncorrection
ERXNFLDSubroutine
"erxnfld"calculatesthemacroscopicreactionfieldenergyarisingfromasetofatomicmultipoles
ERXNFLD1Subroutine
"erxnfld1"calculatesthemacroscopicreactionfieldenergyandderivativeswithrespecttoCartesian
coordinates
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ERXNFLD2Subroutine
"erxnfld2"calculatessecondderivativesofthemacroscopicreactionfieldenergyforasingleatomat
atime
ERXNFLD3Subroutine
"erxnfld3"calculatesthemacroscopicreactionfieldenergy,andalsopartitionstheenergyamongthe
atoms
ESOLVSubroutine
"esolv" calculates the continuum solvation energy via either the Eisenberg-McLachlan ASP model,
Ooi-ScheragaSASAmodel,variousGB/SAmethodsortheACEmodel
ESOLV1Subroutine
"esolv1" calculates the continuum solvation energy and first derivatives with respect to Cartesian
coordinates using either the Eisenberg-McLachlan ASP, Ooi-Scheraga SASA or various GB/SA
solvationmodels
ESOLV2Subroutine
"esolv2"calculatessecondderivativesofthecontinuumsolvationenergyusingeithertheEisenbergMcLachlanASP,Ooi-ScheragaSASAorvariousGB/SAsolvationmodels
ESOLV3Subroutine
"esolv3"calculatesthecontinuumsolvationenergyusingeithertheEisenberg-McLachlanASPmodel,
Ooi-Scheraga SASA model, various GB/SA methods or the ACE model; also partitions the energy
amongtheatoms
ESTRBNDSubroutine
"estrbnd"calculatesthestretch-bendpotentialenergy
ESTRBND1Subroutine
"estrbnd1" calculates the stretch-bend potential energy and first derivatives with respect to
Cartesiancoordinates
ESTRBND2Subroutine
"estrbnd2"calculatesthestretch-bendpotentialenergysecondderivativeswithrespecttoCartesian
coordinates
ESTRBND3Subroutine
"estrbnd3"calculatesthestretch-bendpotentialenergy;alsopartitionstheenergyamongtheatoms
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ESTRTORSubroutine
"estrtor"calculatesthestretch-torsionpotentialenergy
ESTRTOR1Subroutine
"estrtor1" calculates the stretch-torsion energy and first derivatives with respect to Cartesian
coordinates
ESTRTOR2Subroutine
"estrtor2" calculates the stretch-torsion potential energy second derivatives with respect to
Cartesiancoordinates
ESTRTOR3Subroutine
"estrtor3"calculatesthestretch-torsionpotentialenergy;alsopartitionstheenergytermsamongthe
atoms
ETORSSubroutine
"etors"calculatesthetorsionalpotentialenergy
ETORS0ASubroutine
"etors0a"calculatesthetorsionalpotentialenergyusingastandardsumofFourierterms
ETORS0BSubroutine
"etors0b"calculatesthetorsionalpotentialenergyforusewithpotentialenergysmoothingmethods
ETORS1Subroutine
"etors1" calculates the torsional potential energy and first derivatives with respect to Cartesian
coordinates
ETORS1ASubroutine
"etors1a" calculates the torsional potential energy and first derivatives with respect to Cartesian
coordinatesusingastandardsumofFourierterms
ETORS1BSubroutine
"etors1b" calculates the torsional potential energy and first derivatives with respect to Cartesian
coordinatesforusewithpotentialenergysmoothingmethods
ETORS2Subroutine
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"etors2"calculatesthesecondderivativesofthetorsionalenergyforasingleatom
ETORS2ASubroutine
"etors2a"calculatesthesecondderivativesofthetorsionalenergyforasingleatomusingastandard
sumofFourierterms
ETORS2BSubroutine
"etors2b" calculates the second derivatives of the torsional energy for a single atom for use with
potentialenergysmoothingmethods
ETORS3Subroutine
"etors3"calculatesthetorsionalpotentialenergy;alsopartitionstheenergyamongtheatoms
ETORS3ASubroutine
"etors3a" calculates the torsional potential energy using a standard sum of Fourier terms and
partitionstheenergyamongtheatoms
ETORS3BSubroutine
"etors3b"calculatesthetorsionalpotentialenergyforusewithpotentialenergysmoothingmethods
andpartitionstheenergyamongtheatoms
ETORTORSubroutine
"etortor"calculatesthetorsion-torsionpotentialenergy
ETORTOR1Subroutine
"etortor1" calculates the torsion-torsion energy and first derivatives with respect to Cartesian
coordinates
ETORTOR2Subroutine
"etortor2" calculates the torsion-torsion potential energy second derivatives with respect to
Cartesiancoordinates
ETORTOR3Subroutine
"etortor3" calculates the torsion-torsion potential energy; also partitions the energy terms among
theatoms
EUREYSubroutine
"eurey"calculatestheUrey-Bradley1-3interactionenergy
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EUREY1Subroutine
"eurey1" calculates the Urey-Bradley interaction energy and its first derivatives with respect to
Cartesiancoordinates
EUREY2Subroutine
"eurey2"calculatessecondderivativesoftheUrey-Bradleyinteractionenergyforasingleatomata
time
EUREY3Subroutine
"eurey3"calculatestheUrey-Bradleyenergy;alsopartitionstheenergyamongtheatoms
EWALDCOFSubroutine
"ewaldcof" finds a value of the Ewald coefficient such that all terms beyond the specified cutoff
distancewillhaveanvaluelessthanaspecifiedtolerance
EXPLORESubroutine
"explore" uses simulated annealing on an initial crude embedded distance geoemtry structure to
refineversusthebound,chirality,planarityandtorsionalerrorfunctions
EXTRASubroutine
"extra"calculatesanyadditionaluserdefinedpotentialenergycontribution
EXTRA1Subroutine
"extra1"calculatesanyadditionaluserdefinedpotentialenergycontributionanditsfirstderivatives
EXTRA2Subroutine
"extra2" calculates second derivatives of any additional user defined potential energy contribution
forasingleatomatatime
EXTRA3Subroutine
"extra3"calculatesanyadditionaluserdefinedpotentialcontributionandalsopartitionstheenergy
amongtheatoms
FATALSubroutine
"fatal" terminates execution due to a user request, a severe error or some other nonstandard
condition
FFTBACKSubroutine
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FFTFRONTSubroutine
FFTSETUPSubroutine
FIELDSubroutine
"field" sets the force field potential energy functions from a parameter file and modifications
specifiedinakeyfile
FINALSubroutine
"final"performsanyfinalprogramactions,printsastatusmessage,andthenpausesifnecessaryto
avoidclosingtheexecutionwindow
FINDATMSubroutine
"findatm"locatesaspecificPDBatomnametypewithinarangeofatomsfromthePDBfile,returns
zeroifthenametypewasnotfound
FIXPDBSubroutine
"fixpdb"correctsproblemswithPDBfilesbyconvertingresidueandatomnamestotheformsused
byTINKER
FRACDISTSubroutine
"fracdist" computes a normalized distribution of the pairwise fractional distances between the
smoothedupperandlowerbounds
FREEUNITFunction
"freeunit"findsanunopenedFortranI/Ounitandreturnsitsnumericalvaluefrom1to99;theunits
alreadyassignedto"input"and"iout"(usually5and6)areskippedsincetheyhavespecialmeaning
asthedefaultI/Ounits
GAMMLNFunction
"gammln" uses a series expansion due to Lanczos to compute the natural logarithm of the Gamma
functionat"x"in[0,1]
GDAProgram
"gda"implementsGaussianDensityAnnealing(GDA)algorithmforglobaloptimizationviasimulated
annealing
GDA1Subroutine
GDA2Function
GDA3Subroutine
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GDASTATSubroutine
GENDOTSubroutine
"gendot" finds the coordinates of a specified number of surface points for a sphere with the input
radiusandcoordinatecenter
GEODESICSubroutine
"geodesic" smooths the upper and lower distance bounds via the triangle inequality using a sparse
matrixversionofashortestpathalgorithm
GEOMETRYFunction
"geometry"findsthevalueoftheinteratomicdistance,angleordihedralangledefinedbytwotofour
inputatoms
GETBASESubroutine
"getbase" finds the base heavy atoms for a single nucleotide residue and copies the names and
coordinatestotheProteinDataBankfile
GETIMESubroutine
"getime"getselapsedCPUtimeinsecondsforaninterval
GETINTSubroutine
"getint"asksforaninternalcoordinatefilename,thenreadstheinternalcoordinatesandcomputes
Cartesiancoordinates
GETKEYSubroutine
"getkey" finds a valid keyfile and stores its contents as line images for subsequent keyword
parametersearching
GETMOL2Subroutine
"getmol2"asksforaSybylMOL2moleculefilename,thenreadsthecoordinatesfromthefile
GETMONITORSubroutine
GETNUCHSubroutine
"getnuch" finds the nucleotide hydrogen atoms for a single residue and copies the names and
coordinatestotheProteinDataBankfile
GETNUMBSubroutine
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"getnumb" searchs an input string from left to right for an integer and puts the numeric value in
"number";returnszerowith"next"unchangedifnointegervalueisfound
GETPDBSubroutine
"getpdb"asksforaProteinDataBankfilename,thenreadsinthecoordinatesfile
GETPRBSubroutine
"getprb"testsforapossibleprobepositionattheinterfacebetweenthreeneighboringatoms
GETPRMSubroutine
"getprm"findsthepotentialenergyparameterfileandthenopensandreadstheparameters
GETPROHSubroutine
"getproh" finds the hydrogen atoms for a single amino acid residue and copies the names and
coordinatestotheProteinDataBankfile
GETREFSubroutine
"getref" copies structure information from the reference area into the standard variables for the
currentsystemstructure
GETSEQSubroutine
"getseq" asks the user for the amino acid sequence and torsional angle values needed to define a
peptide
GETSEQNSubroutine
"getseqn" asks the user for the nucleotide sequence and torsional angle values needed to define a
nucleicacid
GETSIDESubroutine
"getside"findsthesidechainheavyatomsforasingleaminoacidresidueandcopiesthenamesand
coordinatestotheProteinDataBankfile
GETSTRINGSubroutine
"getstring"searchsforaquotedtextstringwithinaninputcharacterstring;theregionbetweenthe
first and second quotes is returned as the "text"; if the actual text is too long, only the first part is
returned
GETTEXTSubroutine
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"gettext"searchsaninputstringforthefirststringofnon-blankcharacters;theregionfromanonblankcharactertothefirstblankspaceisreturnedas"text";iftheactualtextistoolong,onlythefirst
partisreturned
GETTORSubroutine
"gettor" tests for a possible torus position at the interface between two atoms, and finds the torus
radius,centerandaxis
GETWORDSubroutine
"getword"searchsaninputstringforthefirstalphabeticcharacter(A-Zora-z);theregionfromthis
first character to the first blank space or comma is returned as a "word"; if the actual word is too
long,onlythefirstpartisreturned
GETXYZSubroutine
"getxyz"asksforaCartesiancoordinatefilename,thenreadsinthecoordinatesfile
GRADIENTSubroutine
"gradient" calls subroutines to calculate the potential energy and first derivatives with respect to
Cartesiancoordinates
GRADRGDSubroutine
"gradrgd" calls subroutines to calculate the potential energy and first derivatives with respect to
rigidbodycoordinates
GRADROTSubroutine
"gradrot"callssubroutinestocalculatethepotentialenergyanditstorsionalfirstderivatives
GRAFICSubroutine
"grafic"outputstheupper&lowertrianglesanddiagonalofasquarematrixinaschematicformfor
visualinspection
GROUPSSubroutine
"groups"testsasetofatomstoseeifallaremembersofasingleatomgrouporapairofatomgroups;
ifso,thenthecorrectintra-orintergroupweightisassigned
GRPLINESubroutine
"grpline"testseachatomgroupforlinearityofthesitescontainedinthegroup
GYRATESubroutine
"gyrate"computestheradiusofgyrationofamolecularsystemfromitsatomiccoordinates
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HANGLESubroutine
"hangle"constructshybridanglebendingparametersgivenaninitialstate,finalstateand"lambda"
value
HATOMSubroutine
"hatom"assignsanewatomtypetoeachhybridsite
HBONDSubroutine
"hbond" constructs hybrid bond stretch parameters given an initial state, final state and "lambda"
value
HCHARGESubroutine
"hcharge" constructs hybrid charge interaction parameters given an initial state, final state and
"lambda"value
HDIPOLESubroutine
"hdipole" constructs hybrid dipole interaction parameters given an initial state, final state and
"lambda"value
HESSIANSubroutine
"hessian" calls subroutines to calculate the Hessian elements for each atom in turn with respect to
Cartesiancoordinates
HESSRGDSubroutine
"hessrgd" computes the numerical Hessian elements with respect to rigid body coordinates via
6*ngroup+1gradientevaluations
HESSROTSubroutine
"hessrot"computesthenumericalHessianelementswithrespecttotorsionalangles;eitherthefull
matrix or just the diagonal can be calculated; the full matrix needs nomega+1 gradient evaluations
whilethediagonalrequiresjusttwogradientcalls
HIMPTORSubroutine
"himptor" constructs hybrid improper torsional parameters given an initial state, final state and
"lambda"value
HSTRBNDSubroutine
"hstrbnd"constructshybridstretch-bendparametersgivenaninitialstate,finalstateand"lambda"
value
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HSTRTORSubroutine
"hstrtor"constructshybridstretch-torsionparametersgivenaninitialstate,finalstateand"lambda"
value
HTORSSubroutine
"htors"constructshybridtorsionalparametersforagiveninitialstate,finalstateand"lambda"value
HVDWSubroutine
"hvdw"constructshybridvanderWaalsparametersgivenaninitialstate,finalstateand"lambda"
value
HYBRIDSubroutine
"hybrid" constructs the hybrid hamiltonian for a specified initial state, final state and mutation
parameter"lambda"
IJKPTSSubroutine
"ijkpts"storesasetofindicesusedduringcalculationofmacroscopicreactionfieldenergetics
IMAGESubroutine
"image"takesthecomponentsofpairwisedistancebetweentwopointsinthesameorneighboring
periodicboxesandconvertstothecomponentsoftheminimumimagedistance
IMPOSESubroutine
"impose" performs the least squares best superposition of two atomic coordinate sets via a
quaternion method; upon return, the first coordinate set is unchanged while the second set is
translatedandrotatedtogivebestfit;thefinalrootmeansquarefitisreturnedin"rmsvalue"
INDUCESubroutine
"induce" computes the induced dipole moment at each polarizable site due to direct or mutual
polarization; assumes that multipole components have already been rotated into the global
coordinateframe
INDUCE0ASubroutine
"induce0a" computes the induced dipole moment at each polarizable site using a pairwise double
loop
INDUCE0BSubroutine
"induce0b" computes the induced dipole moment at each polarizable site using a regular Ewald
summation
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INEDGESubroutine
"inedge"insertsaconcaveedgeintothelinkedlistforitstemporarytorus
INERTIASubroutine
"inertia" computes the principal moments of inertia for the system, and optionally translates the
centerofmasstotheoriginandrotatestheprincipalaxesontotheglobalaxes
INITERRFunction
"initerr"istheinitialerrorfunctionandderivativesforadistancegeometryembedding;itincludes
componentsfromthelocalgeometryandtorsionalrestrainterrors
INITIALSubroutine
"initial" sets up original values for some parameters and variables that might not otherwise get
initialized
INITPRMSubroutine
"initprm"completelyinitializesaforcefieldbysettingallparameterstozeroandusingdefaultsfor
controlvalues
INITRESSubroutine
"initres" sets names for biopolymer residue types used in PDB file conversion and automated
generationofstructures
INITROTSubroutine
"initrot" sets the torsional angles which are to be rotated in subsequent computation, by default
automatically selects all rotatable single bonds; assumes internal coordinates have already been
setup
INSERTSubroutine
"insert"addsthespecifiedatomtotheCartesiancoordinateslistandshiftstheremainingatoms
INTEDITProgram
"intedit" allows the user to extract information from or alter the values within an internal
coordinatesfile
INTXYZProgram
"intxyz" takes as input an internal coordinates file, converts to and then writes out Cartesian
coordinates
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INVBETAFunction
"invbeta"computestheinverseBetadistributionfunctionviaacombinationofNewtoniterationand
bisectionsearch
INVERTSubroutine
"invert"invertsamatrixusingtheGauss-Jordanmethod
IPEDGESubroutine
"ipedge"insertsconvexedgeintolinkedlistforatom
ISPLPESubroutine
"isplpe"computesthecoefficientsforacubicperiodicinterpolatingspline
JACOBISubroutine
"jacobi" performs a matrix diagonalization of a real symmetric matrix by the method of Jacobi
rotations
KANGANGSubroutine
"kangang" assigns the parameters for angle-angle cross term interactions and processes new or
changedparametervalues
KANGLESubroutine
"kangle" assigns the force constants and ideal angles for the bond angles; also processes new or
changedparameters
KATOMSubroutine
"katom" assigns an atom type definitions to each atom in the structure and processes any new or
changedvalues
KBONDSubroutine
"kbond"assignsaforceconstantandidealbondlengthtoeachbondinthestructureandprocesses
anyneworchangedparametervalues
KCHARGESubroutine
"kcharge" assigns partial charges to the atoms within the structure and processes any new or
changedvalues
KCHIRALSubroutine
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"kchiral"determinesthetargetvalueforeachchiralityandplanarityrestraintasthesignedvolume
oftheparallelpipedspannedbyvectorsfromacommonatomtoeachofthreeotheratoms
KDIPOLESubroutine
"kdipole"assignsbonddipolestothebondswithinthestructureandprocessesanyneworchanged
values
KENEGSubroutine
"keneg"appliesprimaryandsecondaryelectronegativitybondlengthcorrectionstoapplicablebond
parameters
KEWALDSubroutine
"kewald"assignsbothregularEwaldsummationandparticlemeshEwaldparametersforaperiodic
box
KGEOMSubroutine
"kgeom" asisgns parameters for geometric restraint terms to be included in the potential energy
calculation
KIMPROPSubroutine
"kimprop" assigns potential parameters to each improper dihedral in the structure and processes
anychangedvalues
KIMPTORSubroutine
"kimptor"assignstorsionalparameterstoeachimpropertorsioninthestructureandprocessesany
changedvalues
KINETICSubroutine
"kinetic" computes the total kinetic energy and kinetic energy contributions to the pressure tensor
bysummingovervelocities
KMETALSubroutine
"kmetal" assigns ligand field parameters to transition metal atoms and processes any new or
changedparametervalues
KMPOLESubroutine
"kmpole"assignsatomicmultipolemomentstotheatomsofthestructureandprocessesanynewor
changedvalues
KOPBENDSubroutine
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"kopbend"assignstheforceconstantsforout-of-planebendingattrigonalcentersviaWilson-DeciusCrossanglebends;alsoprocessesanyneworchangedparametervalues
KOPDISTSubroutine
"kopdist"assignstheforceconstantsforout-of-planedistanceattrigonalcentersviathecentralatom
height;alsoprocessesanyneworchangedparametervalues
KORBITSubroutine
"korbit" assigns pi-orbital parameters to conjugated systems and processes any new or changed
parameters
KPITORSSubroutine
"kpitors"assignspi-orbitaltorsionparameterstotorsionsneedingthem,andprocessesanynewor
changedvalues
KPOLARSubroutine
"kpolar" assigns atomic dipole polarizabilities to the atoms within the structure and processes any
neworchangedvalues
KSOLVSubroutine
"ksolv" assigns continuum solvation energy parameters for the Eisenberg-McLachlan ASP, OoiScheragaSASAorvariousGB/SAsolvationmodels
KSTRBNDSubroutine
"kstrbnd" assigns the parameters for the stretch-bend interactions and processes new or changed
parametervalues
KSTRTORSubroutine
"kstrtor" assigns stretch-torsion parameters to torsions needing them, and processes any new or
changedvalues
KTORSSubroutine
"ktors" assigns torsional parameters to each torsion in the structure and processes any new or
changedvalues
KTORTORSubroutine
"ktortor" assigns torsion-torsion parameters to adjacent torsion pairs and processes any new or
changedvalues
KUREYSubroutine
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"kurey" assigns the force constants and ideal distances for the Urey-Bradley 1-3 interactions; also
processesanyneworchangedparametervalues
KVDWSubroutine
"kvdw"assignstheparameterstobeusedincomputingthevanderWaalsinteractionsandprocesses
anyneworchangedvaluesfortheseparameters
LATTICESubroutine
"lattice"storestheperiodicboxdimensionsandsetsanglevaluestobeusedincomputingfractional
coordinates
LBFGSSubroutine
"lbfgs"isalimitedmemoryBFGSquasi-newtonnonlinearoptimizationroutine
LIGASESubroutine
"ligase"translatesanucleicacidstructureinProteinDataBankformattoaCartesiancoordinatefile
andsequencefile
LIGHTSSubroutine
"lights"computesthesetofnearestneighborinteractionsusingthemethodoflightsalgorithm
LINBODYSubroutine
"linbody" finds the angular velocity of a linear rigid body given the inertia tensor and angular
momentum
LMSTEPSubroutine
"lmstep"computestheLevenberg-Marquardtstepduringanonlinearleastsquarescalculation;this
version is based upon ideas from the Minpack routine LMPAR together with with the internal
doublingstrategyofDennisandSchnabel
LOCALMINSubroutine
"localmin" is used during normal mode local search to perform a Cartesian coordinate energy
minimization
LOCALRGDSubroutine
"localrgd"isusedduringthePSSlocalsearchproceduretoperformarigidbodyenergyminimization
LOCALROTSubroutine
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"localrot" is used during the PSS local search procedure to perform a torsional space energy
minimization
LOCALXYZSubroutine
"localxyz" is used during the potential smoothing and search procedure to perform a local
optimizationatthecurrentsmoothinglevel
LOCERRFunction
"locerr"isthelocalgeometryerrorfunctionandderivativesincludingthe1-2,1-3and1-4distance
boundrestraints
LOWCASESubroutine
"lowcase"convertsatextstringtoalllowercaseletters
MAJORIZESubroutine
"majorize" refines the projected coordinates by attempting to minimize the least square residual
betweenthetrialdistancematrixandthedistancescomputedfromthecoordinates
MAKEINTSubroutine
"makeint" converts Cartesian to internal coordinates where selection of internal coordinates is
controlledby"mode"
MAKEPDBSubroutine
"makexyz"convertsasetofCartesiancoordinatestoProteinDataBankformatwithspecialhandling
forsystemsconsistingofpolypeptidechains,ligandsandwatermolecules
MAKEREFSubroutine
"makeref" copies the information contained in the "xyz" file of the current structure into
correspondingreferenceareas
MAKEXYZSubroutine
"makexyz" generates a complete set of Cartesian coordinates for a full structure from the internal
coordinatevalues
MAPCHECKSubroutine
"mapcheck"checksthecurrentminimumenergystructureforpossibleadditiontothemasterlistof
localminima
MAXWELLFunction
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"maxwell" returns a speed in Angstroms/picosecond randomly selected from a 3-D MaxwellBoltzmanndistributionforthespecifiedparticlemassandsystemtemperature
MCM1Function
"mcm1" is a service routine that computes the energy and gradient for truncated Newton
optimizationinCartesiancoordinatespace
MCM2Subroutine
"mcm2"isaserviceroutinethatcomputesthesparsematrixHessianelementsfortruncatedNewton
optimizationinCartesiancoordinatespace
MCMSTEPFunction
"mcmstep"implementstheminimizationphaseofanMCMstepviaCartesianminimizationfollowing
aMonteCarlostep
MDINITSubroutine
"mdinit" initializes the velocities and accelerations for a molecular dynamics trajectory, including
restarts
MDRESTSubroutine
"mdrest" finds and removes any translational or rotational kinetic energy of the overall system
centerofmass
MDSAVESubroutine
"mdsave" writes molecular dynamics trajectory snapshots and auxiliary files with velocity and
induceddipoleinformation;alsochecksforuserrequestedterminationofasimulation
MDSTATSubroutine
"mdstat"iscalledateachmoleculardynamicstimesteptoformstatisticsonvariousaveragevalues
andfluctuations,andtoperiodicallysavethestateofthetrajectory
MEASFNSubroutine
MEASFPSubroutine
MEASFSSubroutine
MEASPMSubroutine
"measpm"computesthevolumeofasingleprismsectionofthefullinteriorpolyhedron
MECHANICSubroutine
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"mechanic"setsupneededparametersforthepotentialenergycalculationandreadsinmanyofthe
userselectableoptions
MERGESubroutine
"merge" combines the reference and current structures into a single new "current" structure
containingthereferenceatomsfollowedbytheatomsofthecurrentstructure
METRICSubroutine
"metric"takesasinputthetrialdistancematrixandcomputesthemetricmatrixofallpossibledot
products between the atomic vectors and the center of mass using the law of cosines and the
followingformulaforthedistancestothecenterofmass:
MIDERRFunction
"miderr" is the secondary error function and derivatives for a distance geometry embedding; it
includes components from the distance bounds, local geometry, chirality and torsional restraint
errors
MINIMIZ1Function
"minimiz1" is a service routine that computes the energy and gradient for a low storage BFGS
optimizationinCartesiancoordinatespace
MINIMIZEProgram
"minimize" performs energy minimization in Cartesian coordinate space using a low storage BFGS
nonlinearoptimization
MINIROTProgram
"minirot" performs an energy minimization in torsional angle space using a low storage BFGS
nonlinearoptimization
MINIROT1Function
"minirot1" is a service routine that computes the energy and gradient for a low storage BFGS
nonlinearoptimizationintorsionalanglespace
MINPATHSubroutine
"minpath"isaroutineforfindingthetrianglesmoothedupperandlowerboundsofeachatomtoa
specifiedrootatomusingasparsevariantoftheBellman-Fordshortestpathalgorithm
MINRIGIDProgram
"minrigid" performs an energy minimization of rigid body atom groups using a low storage BFGS
nonlinearoptimization
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MINRIGID1Function
"minrigid1" is a service routine that computes the energy and gradient for a low storage BFGS
nonlinearoptimizationofrigidbodies
MMIDSubroutine
"mmid" implements a modified midpoint method to advance the integration of a set of first order
differentialequations
MODECARTSubroutine
MODEROTSubroutine
MODESRCHSubroutine
MODETORSSubroutine
MODULISubroutine
"moduli"setsthemodulioftheinversediscreteFouriertransformoftheB-splines;bsmod[1-3]hold
thesevalues,nfft[1-3]arethegriddimensions,bsorderistheorderofB-splineapproximation
MOLECULESubroutine
"molecule"countsthemolecules,assignseachatomtoitsmoleculeandcomputesthemassofeach
molecule
MOLUINDSubroutine
"moluind"computesthemolecularinduceddipolecomponentsinthepresenceofanexternalelectric
field
MOMENTSSubroutine
"moments"computesthetotalelectriccharge,dipoleandquadrupolemomentsfortheentiresystem
asasumoverthepartialcharges,bonddipolesandatomicmultipolemoments
MONTEProgram
"monte"performsaMonteCarlo/MCMconformationalsearchusingeitherCartesiansingleatomor
torsionalmovesets
MUTATESubroutine
"mutate" constructs the hybrid hamiltonian for a specified initial state, final state and mutation
parameter"lambda"
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NEEDUPDATESubroutine
NEIGHBORSubroutine
"neighbor"findsalloftheneighborsofeachatom
NEWATMSubroutine
"newatm"createsanddefinesanatomneededfortheCartesiancoordinatesfile,butwhichmaynot
presentintheoriginalProteinDataBankfile
NEWTONProgram
"newton"performsanenergyminimizationinCartesiancoordinatespaceusingatruncatedNewton
method
NEWTON1Function
"newton1" is a service routine that computes the energy and gradient for truncated Newton
optimizationinCartesiancoordinatespace
NEWTON2Subroutine
"newton2" is a service routine that computes the sparse matrix Hessian elements for truncated
NewtonoptimizationinCartesiancoordinatespace
NEWTROTProgram
"newtrot" performs an energy minimization in torsional angle space using a truncated Newton
conjugategradientmethod
NEWTROT1Function
"newtrot1" is a service routine that computes the energy and gradient for truncated Newton
conjugategradientoptimizationintorsionalanglespace
NEWTROT2Subroutine
"newtrot2" is a service routine that computes the sparse matrix Hessian elements for truncated
Newtonoptimizationintorsionalanglespace
NEXTARGSubroutine
"nextarg"findsthenextunusedcommandlineargumentandreturnsitintheinputcharacterstring
NEXTTEXTFunction
"nexttext"findsandreturnsthelocationofthefirstnon-blankcharacterwithinaninputtextstring;
zeroisreturnedifnosuchcharacterisfound
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NORMALFunction
"normal"generatesarandomnumberfromanormalGaussiandistributionwithameanofzeroanda
varianceofone
NUCBASESubroutine
"nucbase"buildsthesidechainforasinglenucleotidebaseintermsofinternalcoordinates
NUCCHAINSubroutine
"nucchain" builds up the internal coordinates for a nucleic acid sequence from the sugar type,
backboneandglycosidictorsionalvalues
NUCLEICProgram
"nucleic" builds the internal and Cartesian coordinates of a polynucleotide from nucleic acid
sequenceandtorsionalanglevaluesforthenucleicacidbackboneandsidechains
NUMBERFunction
"number"convertsatextnumeralintoanintegervalue;theinputstringmustcontainonlynumeric
characters
NUMERALSubroutine
"numeral" converts an input integer number into the corresponding right- or left-justified text
numeral
NUMGRADSubroutine
"numgrad" computes the gradient of the objective function "fvalue" with respect to Cartesian
coordinatesoftheatomsviaatwo-sidednumericaldifferentiation
OCVMSubroutine
"ocvm" is an optimally conditioned variable metric nonlinear optimization routine without line
searches
OLDATMSubroutine
"oldatm"gettheCartesiancoordinatesforanatomfromtheProteinDataBankfile,thenassignsthe
atomtypeandatomicconnectivities
OPENENDSubroutine
"openend"opensafileonaFortranunitsuchthatthepositionissettothebottomforappendingto
theendofthefile
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OPTIMIZ1Function
"optimiz1" is a service routine that computes the energy and gradient for optimally conditioned
variablemetricoptimizationinCartesiancoordinatespace
OPTIMIZEProgram
"optimize" performs energy minimization in Cartesian coordinate space using an optimally
conditionedvariablemetricmethod
OPTIROTProgram
"optirot" performs an energy minimization in torsional angle space using an optimally conditioned
variablemetricmethod
OPTIROT1Function
"optirot1" is a service routine that computes the energy and gradient for optimally conditioned
variablemetricoptimizationintorsionalanglespace
OPTRIGIDProgram
"optrigid" performs an energy minimization of rigid body atom groups using an optimally
conditionedvariablemetricmethod
OPTRIGID1Function
"optrigid1" is a service routine that computes the energy and gradient for optimally conditioned
variablemetricoptimizationofrigidbodies
OPTSAVESubroutine
"optsave" is used by the optimizers to write imtermediate coordinates and other relevant
information;alsochecksforuserrequestedterminationofanoptimization
ORBITALSubroutine
"orbital" finds and organizes lists of atoms in a pisystem, bonds connecting pisystem atoms and
torsionswhosetwocentralatomsarebothpisystematoms
ORIENTSubroutine
"orient" computes a set of reference Cartesian coordinates in standard orientation for each rigid
bodyatomgroup
ORTHOGSubroutine
"orthog"performsanorthogonalizationofaninputmatrixviathemodifiedGram-Schmidtalgorithm
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OVERLAPSubroutine
"overlap"computestheoverlapfortwoparallelp-orbitalsgiventheatomicnumbersanddistanceof
separation
PARAMYZESubroutine
"paramyze"printstheforcefieldparametersusedinthecomputationofeachofthepotentialenergy
terms
PASSBSubroutine
PASSB2Subroutine
PASSB3Subroutine
PASSB4Subroutine
PASSB5Subroutine
PASSFSubroutine
PASSF2Subroutine
PASSF3Subroutine
PASSF4Subroutine
PASSF5Subroutine
PATHProgram
"path"locatesaseriesofstructuresequallyspacedalongaconformationalpathwayconnectingthe
inputreactantandproductstructures;aseriesofconstrainedoptimizationsorthogonaltothepathis
doneviaLagrangianmultipliers
PATH1Function
PATHPNTSubroutine
"pathpnt"findsastructureonthesynchronoustransitpathwiththespecifiedpathvalue"t"
PATHSCANSubroutine
"pathscan"makesascanofasynchronoustransitpathwaybycomputingstructuresandenergiesfor
specificpathvalues
PATHVALSubroutine
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"pathval"computesthesynchronoustransitpathvalueforthespecifiedstructure
PDBATMSubroutine
"pdbatm"addsanatomtotheProteinDataBankfile
PDBXYZProgram
"pdbxyz" takes as input a Protein Data Bank file and then converts to and writes out a Cartesian
coordinatesfileand,forbiopolymers,asequencefile
PIALTERSubroutine
"pialter" first modifies bond lengths and force constants according to the standard bond slope
parametersandthebondordervaluesstoredin"pnpl";alsoalterssome2-foldtorsionalparameters
basedonthebond-order*betamatrix
PIMOVESubroutine
"pimove"rotatesthevectorbetweenatoms"list(1)"and"list(2)"sothatatom1isattheoriginand
atom 2 along the x-axis; the atoms defining the respective planes are also moved and their bond
lengthsnormalized
PIPLANESubroutine
"piplane"selectsthethreeatomswhichspecifytheplaneperpendiculartoeachp-orbital;thecurrent
versionwillfailincertainsituations,includingketenes,allenes,andisolatedoradjacenttriplebonds
PISCFSubroutine
"piscf"performsanscfmolecularorbitalcalculationforthepisystemusingamodifiedPariser-ParrPoplemethod
PITILTSubroutine
"pitilt"calculatesforeachpibondtheratiooftheactualp-orbitaloverlapintegraltotheidealoverlap
ifthesameorbitalswereperfectlyparallel
PLACESubroutine
"place"findstheprobesitesbyputtingtheprobespheretangenttoeachtripleofneighboringatoms
POLARGRPSubroutine
"polargrp"generatesmembersofthepolarizationgroupofeachatomandseparatelistsofthe1-2,13and1-4groupconnectivities
POLARIZEProgram
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"polarize" computes the molecular polarizability by applying an external field along each axis
followedbydiagonalizationoftheresultingpolarizabilitytensor
POLYMERSubroutine
"polymer"testsforthepresenceofaninfinitepolymerextendingacrossperiodicboundaries
POLYPSubroutine
"polyp"isapolynomialproductroutinethatmultipliestwoalgebraicforms
POTNRGFunction
POTOFFSubroutine
"potoff"clearstheforcefielddefinitionbyturningofftheuseofeachofthepotentialenergyfunctions
POWERSubroutine
"power" uses the power method with deflation to compute the few largest eigenvalues and
eigenvectorsofasymmetricmatrix
PRECISEFunction
"precise"findsamachineprecisionvalueasselectedbytheinputargument:(1)thesmallestpositive
floating point value, (2) the smallest relative floating point spacing, (3) the largest relative floating
pointspacing
PRECONDSubroutine
"precond" solves a simplified version of the Newton equations Ms = r, and uses the result to
preconditionlinearconjugategradientiterationsonthefullNewtonequationsin"tnsolve"
PRESSURESubroutine
"pressure" uses the internal virial to find the pressure in a periodic box and maintains a constant
desiredpressurebyscalingthecoordinatesviacouplingtoanexternalconstantpressurebath
PRMKEYSubroutine
"field"parsesatextstringtoextractkeywordsrelatedtoforcefieldpotentialenergyfunctionalforms
andconstants
PROCHAINSubroutine
"prochain" builds up the internal coordinates for an amino acid sequence from the phi, psi, omega
andchivalues
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PROJCTSubroutine
PROMOSubroutine
"promo"writesashortmessagecontaininginformationabouttheTINKERversionnumberandthe
copyrightnotice
PROPERTYFunction
"property" takes two input snapshot frames and computes the value of the property for which the
correlationfunctionisbeingaccumulated
PROPYZESubroutine
"propyze" finds and prints the total charge, dipole moment components, radius of gyration and
momentsofinertia
PROSIDESubroutine
"proside"buildsthesidechainforasingleaminoacidresidueintermsofinternalcoordinates
PROTEINProgram
"protein" builds the internal and Cartesian coordinates of a polypeptide from amino acid sequence
andtorsionalanglevaluesforthepeptidebackboneandsidechains
PRTARCSubroutine
"prtarc" writes out a set of Cartesian coordinates for all active atoms in the TINKER XYZ archive
format
PRTCARSubroutine
"prtcar"writesoutasetofCartesiancoordinatesforallactiveatomsintheAccelerysInsightII.car
format
PRTDYNSubroutine
"prtdyn"writesouttheinformationneededtorestartamoleculardynamicstrajectorytoanexternal
diskfile
PRTERRSubroutine
"prterr"writesoutasetofcoordinatestoadiskfilepriortoabortingonaseriouserror
PRTINTSubroutine
"prtint"writesoutasetofZ-matrixinternalcoordinatestoanexternaldiskfile
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PRTMOL2Program
"prtmol2"writesoutasetofcoordinatesinSybylMOL2formattoanexternaldiskfile
PRTPDBSubroutine
"prtpdb"writesoutasetofProteinDataBankcoordinatestoanexternaldiskfile
PRTPRMSubroutine
"prtprm"writesoutaformattedlistingofthedefaultsetofpotentialenergyparametersforaforce
field
PRTSEQSubroutine
"prtseq" writes out a biopolymer sequence to an external disk file with 15 residues per line and
distinctchainsseparatedbyblanklines
PRTXMOLSubroutine
"prtxmol" writes out a set of Cartesian coordinates for all active atoms in a simple, generic XYZ
formatoriginallyusedbytheXMOLprogram
PRTXYZSubroutine
"prtxyz"writesoutasetofCartesiancoordinatestoanexternaldiskfile
PSSProgram
"pss" implements the potential smoothing plus search method for global optimization in Cartesian
coordinatespacewithlocalsearchesperformedinCartesianortorsionalspace
PSS1Function
"pss1"isaserviceroutinethatcomputestheenergyandgradientduringPSSglobaloptimizationin
Cartesiancoordinatespace
PSS2Subroutine
"pss2" is a service routine that computes the sparse matrix Hessian elements during PSS global
optimizationinCartesiancoordinatespace
PSSRGD1Function
"pssrgd1"isaserviceroutinethatcomputestheenergyandgradientduringPSSglobaloptimization
overrigidbodies
PSSRIGIDProgram
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"pssrigid"implementsthepotentialsmoothingplussearchmethodforglobaloptimizationforasetof
rigidbodies
PSSROTProgram
"pssrot"implementsthepotentialsmoothingplussearchmethodforglobaloptimizationintorsional
space
PSSROT1Function
"pssrot1"isaserviceroutinethatcomputestheenergyandgradientduringPSSglobaloptimization
intorsionalspace
PSSWRITESubroutine
PTINCYFunction
PZEXTRSubroutine
"pzextr" is a polynomial extrapolation routine used during Bulirsch-Stoer integration of ordinary
differentialequations
QRFACTSubroutine
"qrfact" performs Householder transformations with column pivoting (optional) to compute a QR
factorizationofthembynmatrixa;theroutinedeterminesanorthogonalmatrixq,apermutation
matrixp,andanuppertrapezoidalmatrixrwithdiagonalelementsofnonincreasingmagnitude,such
thata*p=q*r;theHouseholdertransformationforcolumnk,k=1,2,...,min(m,n),isoftheform
QRSOLVESubroutine
"qrsolve" solves a*x=b and d*x=0 in the least squares sense; normally used in combination with
routine"qrfact"tosolveleastsquaresproblems
QUATFITSubroutine
"quatfit" uses a quaternion-based method to achieve the best fit superposition of two sets of
coordinates
RADIALProgram
"radial"findstheradialdistributionfunctionforaspecifiedpairofatomtypesviaanalysisofasetof
coordinateframes
RANDOMFunction
"random" generates a random number on [0,1] via a long period generator due to L'Ecuyer with
Bays-Durhamshuffle
RANVECSubroutine
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"ranvec" generates a unit vector in 3-dimensional space with uniformly distributed random
orientation
RATTLESubroutine
"rattle"implementsthefirstportionoftherattlealgorithmbycorrectingatomicpositionsandhalfstepvelocitiestomaintaininteratomicdistanceandabsolutespatialconstraints
RATTLE2Subroutine
"rattle2"implementsthesecondportionoftherattlealgorithmbycorrectingthefull-stepvelocities
inordertomaintaininteratomicdistanceconstraints
READBLKSubroutine
"readblk"readsinasetofsnapshotframesandtransfersthevaluestointernalarraysforuseinthe
computationoftimecorrelationfunctions
READDYNSubroutine
"readdyn" get the positions, velocities and accelerations for a molecular dynamics restart from an
externaldiskfile
READINTSubroutine
"readint"getsasetofZ-matrixinternalcoordinatesfromanexternalfile
READMOL2Subroutine
"readmol2"getsasetofSybylMOL2coordinatesfromanexternaldiskfile
READPDBSubroutine
"readpdb"getsasetofProteinDataBankcoordinatesfromanexternaldiskfile
READPRMSubroutine
"readprm" processes the potential energy parameter file in order to define the default force field
parameters
READSEQSubroutine
"readseq"getsabiopolymersequencecontainingoneormoreseparatechainsfromanexternalfile;
alllinescontainingsequencemustbeginwiththestartingsequencenumber,theactualsequenceis
readfromsubsequentnonblankcharacters
READXYZSubroutine
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"readxyz"getsasetofCartesiancoordinatesfromanexternaldiskfile
REFINESubroutine
"refine" performs minimization of the atomic coordinates of an initial crude embedded distance
geometrystructureversusthebound,chirality,planarityandtorsionalerrorfunctions
RELEASEMONITORSubroutine
REPLICASubroutine
"replica"decidesbetweenimagesandreplicatesforgenerationofperiodicboundaryconditions,and
setsthecellreplicatelistifthereplicatesmethodistobeused
RFINDEXSubroutine
"rfindex"findsindicesforeachmultipolesiteforuseincomputingreactionfieldenergetics
RGDSRCHSubroutine
RGDSTEPSubroutine
"rgdstep"performsasinglemoleculardynamicstimestepforarigidbodycalculation
RIBOSOMESubroutine
"ribosome"translatesapolypeptidestructureinProteinDataBankformattoaCartesiancoordinate
fileandsequencefile
RIGIDXYZSubroutine
"rigidxyz" computes Cartesian coordinates for a rigid body group via rotation and translation of
referencecoordinates
RINGSSubroutine
"rings"searchesthestructureforsmallringsandstorestheirconstituentatoms
RMSERRORSubroutine
"rmserror" computes the maximum absolute deviation and the rms deviation from the distance
bounds,andthenumberandrmsvalueofthedistancerestraintviolations
RMSFITFunction
"rmsfit"computesthermsfitoftwocoordinatesets
ROTANGFunction
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ROTCHECKFunction
"rotcheck" tests a specified candidate rotatable bond for the disallowed case where inactive atoms
arefoundonbothsidesofthecandidatebond
ROTEULERSubroutine
"roteuler"computesasetofEuleranglevaluesconsistentwithaninputrotationmatrix
ROTLISTSubroutine
"rotlist" generates the minimum list of all the atoms lying to one side of a pair of directly bonded
atoms;optionallyfindstheminimallistbychoosingthesidewithfeweratoms
ROTMATSubroutine
"rotmat"findstherotationmatrixthatconvertsfromthelocalcoordinatesystemtotheglobalframe
atamultipolesite
ROTPOLESubroutine
"rotpole"constructsthesetofatomicmultipolesintheglobalframebyapplyingthecorrectrotation
matrixforeachsite
ROTRGDSubroutine
"rotrgd"findstherotationmatrixforarigidbodyduetoasinglestepofdynamics
ROTSITESubroutine
"rotsite" computes the atomic multipoles at a specified site in the global coordinate frame by
applyingarotationmatrix
SADDLEProgram
"saddle" finds a transition state between two conformational minima using a combination of ideas
fromthesynchronoustransit(Halgren-Lipscomb)andquadraticpath(Bell-Crighton)methods
SADDLE1Function
"saddle1"isaserviceroutinethatcomputestheenergyandgradientfortransitionstateoptimization
SADDLESSubroutine
"saddles"constructscircles,convexedgesandsaddlefaces
SCANProgram
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"scan" attempts to find all the local minima on a potential energy surface via an iterative series of
localsearches
SCAN1Function
"scan1"isaserviceroutinethatcomputestheenergyandgradientduringexplorationofapotential
energysurfaceviaiterativelocalsearch
SCAN2Subroutine
"scan2"isaserviceroutinethatcomputesthesparsematrixHessianelementsduringexplorationof
apotentialenergysurfaceviaiterativelocalsearch
SDAREASubroutine
"sdarea"optionallyscalestheatomicfrictioncoefficientofeachatombasedonitsaccessiblesurface
area
SDSTEPSubroutine
"sdstep"performsasinglestochasticdynamicstimestepviaavelocityVerletintegrationalgorithm
SDTERMSubroutine
"sdterm" gets frictional and random force terms needed to update positions and velocities via
stochasticdynamics
SEARCHSubroutine
"search"isaunidimensionallinesearchbaseduponparabolicextrapolationandcubicinterpolation
usingbothfunctionandgradientvalues;ifforcedtosearchinanuphilldirection,returnisafterthe
initialstep
SETACCELERATIONSubroutine
SETATOMICSubroutine
SETATOMTYPESSubroutine
SETCHARGESubroutine
SETCONNECTIVITYSubroutine
SETCOORDINATESSubroutine
SETENERGYSubroutine
SETFILESubroutine
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SETFORCEFIELDSubroutine
SETGRADIENTSSubroutine
SETIMESubroutine
"setime"initializestheelapsedintervalCPUtimer
SETINDUCEDSubroutine
SETKEYWORDSubroutine
SETMASSSubroutine
SETNAMESubroutine
SETSTEPSubroutine
SETSTORYSubroutine
SETTIMESubroutine
SETUPDATEDSubroutine
SETVELOCITYSubroutine
SHAKEUPSubroutine
"shakeup" initializes any holonomic constraints for use with the rattle algorithm during molecular
dynamics
SIGMOIDFunction
"sigmoid"implementsanormalizedsigmoidalfunctionontheinterval[0,1];thecurvesconnect(0,0)
to(1,1)andhaveacooperativitycontrolledbybeta,theyapproachastraightlineasbeta->0andget
morenonlinearasbetaincreases
SKTDYNSubroutine
"sktdyn"sendsthecurrentdynamicsinfoviaasocket
SKTINITSubroutine
"sktinit" sets up socket communication with the graphical user interface by starting a Java virtual
machine,initiatingaserver,andloadinganobjectwithsysteminformation
SKTKILLSubroutine
"sktkill"closestheserverandJavavirtualmachine
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SKTOPTSubroutine
"sktopt"sendsthecurrentoptimizationinfoviaasocket
SLATERSubroutine
"slater"isageneralroutineforcomputingtheoverlapintegralsbetweentwoSlater-typeorbitals
SMOOTHSubroutine
"smooth" sets the type of smoothing method and the extent of surface deformation for use with
potentialenergysmoothing
SNIFFERProgram
"sniffer"performsaglobalenergyminimizationusingadiscreteversionofGriewank'sglobalsearch
trajectory
SNIFFER1Function
"sniffer1" is a service routine that computes the energy and gradient for the Sniffer global
optimizationmethod
SOAKSubroutine
"soak"takesacurrentlydefinedsolutesystemandplacesitintoasolventbox,withremovalofany
solventmoleculesthatoverlapthesolute
SORTSubroutine
"sort"takesaninputlistofintegersandsortsitintoascendingorderusingtheHeapsortalgorithm
SORT10Subroutine
"sort10"takesaninputlistofcharacterstringsandsortsitintoalphabeticalorderusingtheHeapsort
algorithm,duplicatevaluesareremovedfromthefinalsortedlist
SORT2Subroutine
"sort2"takesaninputlistofrealsandsortsitintoascendingorderusingtheHeapsortalgorithm;it
alsoreturnsakeyintotheoriginalordering
SORT3Subroutine
"sort3"takesaninputlistofintegersandsortsitintoascendingorderusingtheHeapsortalgorithm;
italsoreturnsakeyintotheoriginalordering
SORT4Subroutine
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"sort4"takesaninputlistofintegersandsortsitintoascendingabsolutevalueusingtheHeapsort
algorithm
SORT5Subroutine
"sort5"takesaninputlistofintegersandsortsitintoascendingorderbasedoneachvaluemodulo
"m"
SORT6Subroutine
"sort6"takesaninputlistofcharacterstringsandsortsitintoalphabeticalorderusingtheHeapsort
algorithm
SORT7Subroutine
"sort7"takesaninputlistofcharacterstringsandsortsitintoalphabeticalorderusingtheHeapsort
algorithm;italsoreturnsakeyintotheoriginalordering
SORT8Subroutine
"sort8"takesaninputlistofintegersandsortsitintoascendingorderusingtheHeapsortalgorithm,
duplicatevaluesareremovedfromthefinalsortedlist
SORT9Subroutine
"sort9" takes an input list of reals and sorts it into ascending order using the Heapsort algorithm,
duplicatevaluesareremovedfromthefinalsortedlist
SPACEFILLProgram
"spacefill" computes the surface area and volume of a structure; the van der Waals, accessibleexcluded,andcontact-reentrantdefinitionsareavailable
SPECTRUMProgram
"spectrum"computesapowerspectrumoverawavelengthrangefromthevelocityautocorrelation
asafunctionoftime
SQUARESubroutine
"square" is a nonlinear least squares routine derived from the IMSL routine BCLSF and More's
MinpackroutineLMDER;theJacobianisestimatedbyfinitedifferencesandboundscanbespecified
forthevariablestoberefined
SUFFIXSubroutine
"suffix"checksafilenameforthepresenceofanextension,andappendsanextensionifnoneisfound
SUPERPOSEProgram
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"superpose"takespairsofstructuresandsuperimposesthemintheoptimalleastsquares sense;it
willattempttomatchallatompairsoronlythosespecifiedbytheuser
SURFACESubroutine
"surface"performsananalyticalcomputationoftheweightedsolventaccessiblesurfaceareaofeach
atomandthefirstderivativesoftheareawithrespecttoCartesiancoordinates
SURFATOMSubroutine
"surfatom"performsananalyticalcomputationofthesurfaceareaofaspecifiedatom;asimplified
versionof"surface"
SWITCHSubroutine
"switch"setsthecoeffcientsusedbythefifthandseventhorderpolynomialswitchingfunctionsfor
sphericalcutoffs
SYBYLXYZProgram
"sybylxyz" takes as input a Sybyl MOL2 coordinates file, converts to and then writes out Cartesian
coordinates
SYMMETRYSubroutine
"symmetry" applies symmetry operators to the fractional coordinates of the asymmetric unit in
ordertogeneratethesymmetryrelatedatomsofthefullunitcell
TANGENTSubroutine
"tangent"findstheprojectedgradientonthesynchronoustransitpathforapointalongthetransit
pathway
TEMPERSubroutine
"temper"appliesavelocitycorrectionatthehalftimestepasneededfortheNose-Hooverextended
systemthermostat
TEMPER2Subroutine
"temper2"computestheinstantaneoustemperatureandappliesathermostatviaBerendsenvelocity
scaling,Andersenstochasticcollisions,LangevinpistonorNose-Hooverextendedsystems
TESTGRADProgram
"testgrad" computes and compares the analytical and numerical gradient vectors of the potential
energyfunctionwithrespecttoCartesiancoordinates
TESTHESSProgram
131
TINKERUser'sGuide
131
"testhess" computes and compares the analytical and numerical Hessian matrices of the potential
energyfunctionwithrespecttoCartesiancoordinates
TESTLIGHTProgram
"testlight" performs a set of timing tests to compare the evaluation of potential energy and
energy/gradientusingthemethodoflightswithadoubleloopoverallatompairs
TESTROTProgram
"testrot" computes and compares the analytical and numerical gradient vectors of the potential
energyfunctionwithrespecttorotatabletorsionalangles
TIMERProgram
"timer"measurestheCPUtimerequiredforfilereadingandparameterassignment,potentialenergy
computation,energyandgradientcomputation,andHessianmatrixevaluation
TIMEROTProgram
"timerot" measures the CPU time required for file reading and parameter assignment, potential
energy computation, energy and gradient over torsions, and torsional angle Hessian matrix
evaluation
TNCGSubroutine
"tncg" implements a truncated Newton optimization algorithm in which a preconditioned linear
conjugate gradient method is used to approximately solve Newton's equations; special features
include use of an explicit sparse Hessian or finite-difference gradient-Hessian products within the
PCG iteration; the exact Newton search directions can be used optionally; by default the algorithm
checks for negative curvature to prevent convergence to a stationary point having negative
eigenvalues;ifasaddlepointisdesiredthistestcanberemovedbydisabling"negtest"
TNSOLVESubroutine
"tnsolve"usesalinearconjugategradientmethodtofindanapproximatesolutiontothesetoflinear
equationsrepresentedinmatrixformbyHp=-g(Newton'sequations)
TORPHASESubroutine
"torphase" sets the n-fold amplitude and phase values for each torsion via sorting of the input
parameters
TORQUESubroutine
"torque"takesthetorquevaluesonsitesdefinedbylocalcoordinateframesanddistributesthmeto
converttoforcesontheoriginalsitesandsitesspecifyingthelocalframes
TORQUE1Subroutine
132
TINKERUser'sGuide
132
"torque1" takes the torque value on a site defined by a local coordinate frame and distributes it to
converttoforcesontheoriginalsiteandsitesspecifyingthelocalframe
TORSERFunction
"torser" computes the torsional error function and its first derivatives with respect to the atomic
Cartesian coordinates based on the deviation of specified torsional angles from desired values, the
containedbondanglesarealsorestrainedtoavoidanumericalinstability
TORSIONSSubroutine
"torsions"findsthetotalnumberofdihedralanglesandthenumbersofthefouratomsdefiningeach
dihedralangle
TORUSSubroutine
"torus"setsalistofallofthetemporarytoruspositionsbytestingforatorusbetweeneachatomand
itsneighbors
TOTERRFunction
"toterr" is the error function and derivatives for a distance geometry embedding; it includes
componentsfromthedistancebounds,hardspherecontacts,localgeometry,chiralityandtorsional
restrainterrors
TRANSITFunction
"transit"evaluatesthesynchronoustransitfunctionandgradient;linearandquadratictransitpaths
areavailable
TRIANGLESubroutine
"triangle" smooths the upper and lower distance bounds via the triangle inequality using a fullmatrix variant of the Floyd-Warshall shortest path algorithm; this routine is usually much slower
thanthesparsematrixshortestpathmethodsin"geodesic"and"trifix",andshouldbeusedonlyfor
comparisonwithanswersgeneratedbythoseroutines
TRIFIXSubroutine
"trifix" rebuilds both the upper and lower distance bound matrices following tightening of one or
both of the bounds between a specified pair of atoms, "p" and "q", using a modification of
Murchland'sshortestpathupdatealgorithm
TRIMTEXTFunction
"trimtext"findsandreturnsthelocationofthelastnon-blankcharacterbeforethefirstnullcharacter
inaninputtextstring;thefunctionreturnszeroifnosuchcharacterisfound
TRIPLEFunction
133
TINKERUser'sGuide
133
"triple" finds the triple product of three vectors; used as a service routine by the Connolly surface
areaandvolumecomputation
TRUSTSubroutine
"trust"updatesthemodeltrustregionforanonlinearleastsquarescalculation;thisversionisbased
ontheideasfoundinNL2SOLandinDennisandSchnabel'sbook
UDIRECT1Subroutine
"udirect1"computesthereciprocalspacecontributionofthepermanentatomicmultipolemoments
to the electrostatic field for use in finding the direct induced dipole moments via a regular Ewald
summation
UDIRECT2Subroutine
"udirect2"computestherealspacecontributionofthepermanentatomicmultipolemomentstothe
electrostatic field for use in finding the direct induced dipole moments via a regular Ewald
summation
UFIELDSubroutine
"ufield" finds the field at each polarizable site due to the induced dipoles at the other sites using
Thole'smethodtodampthefieldatcloserange
UMUTUAL1Subroutine
"umutual1"computesthereciprocalspacecontributionoftheinducedatomicdipolemomentstothe
electrostatic field for use in iterative calculation of induced dipole moments via a regular Ewald
summation
UMUTUAL2Subroutine
"umutual2" computes the real space contribution of the induced atomic dipole moments to the
electrostatic field for use in iterative calculation of induced dipole moments via a regular Ewald
summation
UNITCELLSubroutine
"unitcell"getstheperiodicboundaryboxsizeandrelatedvaluesfromanexternalkeywordfile
UPCASESubroutine
"upcase"convertsatextstringtoalluppercaseletters
VAMSubroutine
"vam" takes the analytical molecular surface defined as a collection of spherical and toroidal
polygonsandusesittocomputethevolumeandsurfacearea
134
TINKERUser'sGuide
134
VCROSSSubroutine
"vcross"findsthecrossproductoftwovectors
VDWERRFunction
"vdwerr"isthehardspherevanderWaalsbounderrorfunctionandderivativesthatpenalizesclose
nonbondedcontacts,pairwiseneighborsaregeneratedviathemethodoflights
VECANGFunction
"vecang"findstheanglebetweentwovectorshandedwithrespecttoacoordinateaxis;returnsan
angleintherange[0,2*pi]
VERLETSubroutine
"verlet" performs a single molecular dynamics time step by means of the velocity Verlet multistep
recursionformula
VERSIONSubroutine
"version" checks the name of a file about to be opened; if if "old" status is passed, the name of the
highest current version is returned; if "new" status is passed the filename of the next available
unusedversionisgenerated
VIBRATEProgram
"vibrate" performs a vibrational normal mode analysis; the Hessian matrix of second derivatives is
determined and then diagonalized both directly and after mass weighting; output consists of the
eigenvaluesoftheforceconstantmatrixaswellasthevibrationalfrequenciesanddisplacements
VIBRIGIDProgram
"vibrigid"computestheeigenvaluesandeigenvectorsoftheHessianmatrixoverrigidbodydegrees
offreedom
VIBROTProgram
"vibrot"computestheeigenvaluesandeigenvectorsofthetorsionalHessianmatrix
VNORMSubroutine
"vnorm" normalizes a vector to unit length; used as a service routine by the Connolly surface area
andvolumecomputation
VOLUMESubroutine
"volume" calculates the excluded volume via the Connolly analytical volume and surface area
algorithm
135
TINKERUser'sGuide
135
VOLUME1Subroutine
"volume1" calculates first derivatives of the total excluded volume with respect to the Cartesian
coordinatesofeachatom
VOLUME2Subroutine
"volume2" calculates second derivatives of the total excluded volume with respect to the Cartesian
coordinatesoftheatoms
WATSONSubroutine
"watson"usesarigidbodyoptimizationtoapproximatelyalignthepairedstrandsofanucleicacid
doublehelix
WATSON1Function
"watson1" is a service routine that computes the energy and gradient for optimally conditioned
variablemetricoptimizationofrigidbodies
XTALERRSubroutine
"xtalerr" computes an error function value derived from derivatives with respect to lattice
parameters,latticeenergyandmonomerdipolemoments
XTALFITProgram
"xtalfit"computesanoptimizedsetofpotentialenergyparametersforuserspecifiedvanderWaals
and electrostatic interactions by fitting to crystal structure, lattice energy and monomer dipole
momentdata
XTALLAT1Function
"xtalmol1"isaserviceroutinethatcomputestheenergyandnumericalgradientwithrespecttothe
sixlatticelengthsandanglesforacrystalenergyminimization
XTALMINProgram
"xtalmin" performs a full crystal energy minimization by alternating cycles of truncated Newton
optimization over atomic coordinates with variable metric optimization over the six lattice
dimensionsandangles
XTALMOL1Function
"xtalmol1" is a service routine that computes the energy and gradient with respect to the atomic
Cartesiancoordinatesforacrystalenergyminimization
XTALMOL2Subroutine
136
TINKERUser'sGuide
136
"xtalmol2"isaserviceroutinethatcomputesthesparsematrixHessianelementswithrespecttothe
atomicCartesiancoordinatesforacrystalenergyminimization
XTALMOVESubroutine
"xtalmove" converts fractional to Cartesian coordinates for rigid molecules during fitting of force
fieldparameterstocrystalstructuredata
XTALPRMSubroutine
"xtalprm" stores or retrieves a crystal structure; used to make a previously stored structure the
currentlyactivestructure,ortostoreastructureforlateruse;onlyprovidesfortheintermolecular
energyterms
XTALWRTSubroutine
"xtalwrt"isautilitythatprintsintermediateresultsduringfittingofforcefieldparameterstocrystal
data
XYZATMSubroutine
"xyzatm"computestheCartesiancoordinatesofasingleatomfromitsdefininginternalcoordinate
values
XYZEDITProgram
"xyzedit"providesformodificationandmanipulationofthecontentsofaCartesiancoordinatesfile
XYZINTProgram
"xyzint" takes as input a Cartesian coordinates file, then converts to and writes out an internal
coordinatesfile
XYZPDBProgram
"xyzpdb"takesasinputaCartesiancoordinatesfile,thenconvertstoandwritesoutaProteinData
Bankfile
XYZRIGIDSubroutine
"xyzrigid"computesthecenterofmassandEuleranglerigidbodycoordinatesforeachatomgroup
inthesystem
XYZSYBYLProgram
"xyzsybyl"takesasinputaCartesiancoordinatesfile,convertstoandthenwritesoutaSybylMOL2
file
ZATOMSubroutine
137
TINKERUser'sGuide
137
"zatom"addsanatomtotheendofthecurrentZ-matrixandthenincrementstheatomcounter;atom
type,definingatomsandinternalcoordinatesarepassedasarguments
ZHELPSubroutine
"zhelp"printsthegeneralinformationandinstructionsfortheZ-matrixeditingprogram
ZVALUESubroutine
"zvalue" gets user supplied values for selected coordinates as needed by the internal coordinate
editingprogram
138
TINKERUser'sGuide
138
10.
DescriptionsofGlobalVariables
The Fortran common blocks found in the TINKER package are listed below along with a brief
descriptionofthecontentsofeachvariableineachcommonblock.Eachindividualcommonblockis
presentasaseparate".i"fileinthe/sourcesubdirectory.Asourcecodelistingcontainingeachofthe
sourcecodemodulesandeachofthecommonblockscanbeproducedbyrunningthe"listing.make"
scriptfoundinthedistribution.
ACTION
totalnumberofeachenergytermcomputed
neb
nea
neba
neub
neaa
neopb
neopd
neid
neit
net
nept
nebt
nett
nev
nec
necd
ned
nem
nep
new
ner
nes
nelf
neg
nex
numberofbondstretchenergytermscomputed
numberofanglebendenergytermscomputed
numberofstretch-bendenergytermscomputed
numberofUrey-Bradleyenergytermscomputed
numberofangle-angleenergytermscomputed
numberofout-of-planebendenergytermscomputed
numberofout-of-planedistanceenergytermscomputed
numberofimproperdihedralenergytermscomputed
numberofimpropertorsionenergytermscomputed
numberoftorsionalenergytermscomputed
numberofpi-orbitaltorsionenergytermscomputed
numberofstretch-torsionenergytermscomputed
numberoftorsion-torsionenergytermscomputed
numberofvanderWaalsenergytermscomputed
numberofcharge-chargeenergytermscomputed
numberofcharge-dipoleenergytermscomputed
numberofdipole-dipoleenergytermscomputed
numberofmultipoleenergytermscomputed
numberofpolarizationenergytermscomputed
numberofEwaldsummationenergytermscomputed
numberofreactionfieldenergytermscomputed
numberofsolvationenergytermscomputed
numberofmetalligandfieldenergytermscomputed
numberofgeometricrestraintenergytermscomputed
numberofextraenergytermscomputed
ALIGN
informationforsuperpositionofstructures
wfit
nfit
ifit
weightsassignedtoatompairsduringsuperposition
numberofatomstouseinsuperimposingtwostructures
atomnumbersofpairsofatomstobesuperimposed
ANALYZ
energycomponentspartitionedoveratoms
aesum
aeb
aea
aeba
aeub
aeaa
aeopb
totalpotentialenergypartitionedoveratoms
bondstretchenergypartitionedoveratoms
anglebendenergypartitionedoveratoms
stretch-bendenergypartitionedoveratoms
Urey-Bradleyenergypartitionedoveratoms
angle-angleenergypartitionedoveratoms
out-of-planebendenergypartitionedoveratoms
139
TINKERUser'sGuide
139
aeopd
aeid
aeit
aet
aept
aebt
aett
aev
aec
aecd
aed
aem
aep
aer
aes
aelf
aeg
aex
out-of-planedistanceenergypartitionedoveratoms
improperdihedralenergypartitionedoveratoms
impropertorsionenergypartitionedoveratoms
torsionalenergypartitionedoveratoms
pi-orbitaltorsionenergypartitionedoveratoms
stretch-torsionenergypartitionedoveratoms
torsion-torsionenergypartitionedoveratoms
vanderWaalsenergypartitionedoveratoms
charge-chargeenergypartitionedoveratoms
charge-dipoleenergypartitionedoveratoms
dipole-dipoleenergypartitionedoveratoms
multipoleenergypartitionedoveratoms
polarizationenergypartitionedoveratoms
reactionfieldenergypartitionedoveratoms
solvationenergypartitionedoveratoms
metalligandfieldenergypartitionedoveratoms
geometricrestraintenergypartitionedoveratoms
extraenergytermpartitionedoveratoms
ANGANG
angle-angletermsincurrentstructure
kaa
nangang
iaa
forceconstantforangle-anglecrossterms
totalnumberofangle-angleinteractions
anglenumbersusedineachangle-angleterm
ANGLE
bondangleswithinthecurrentstructure
ak
anat
afld
nangle
iang
angtyp
harmonicangleforceconstant(kcal/mole/rad**2)
idealbondangleorphaseshiftangle(degrees)
periodicityforFourierbondangleterm
totalnumberofbondanglesinthesystem
numbersoftheatomsineachbondangle
potentialenergyfunctiontypeforeachbondangle
ANGPOT
specificsofbondanglefunctionalforms
cang
qang
pang
sang
angunit
stbnunit
aaunit
opbunit
opdunit
mm2stbn
cubiccoefficientinanglebendingpotential
quarticcoefficientinanglebendingpotential
quinticcoefficientinanglebendingpotential
sexticcoefficientinanglebendingpotential
convertanglebendingenergytokcal/mole
convertstretch-bendenergytokcal/mole
convertangle-angleenergytokcal/mole
convertout-of-planebendenergytokcal/mole
convertout-of-planedistanceenergytokcal/mole
logicalflaggoverninguseofMM2-stylestretch-bend
ARGUE
commandlineargumentsatprogramstartup
maxarg
narg
listarg
maximumnumberofcommandlinearguments
numberofcommandlineargumentstotheprogram
flagtomarkavailablecommandlinearguments
140
TINKERUser'sGuide
140
arg
stringscontainingthecommandlinearguments
ATMLST
localgeometrytermsinvolvingeachatom
bndlist
anglist
listofthebondnumbersinvolvingeachatom
listoftheanglenumberscenteredoneachatom
ATMTYP
atomicpropertiesforeachcurrentatom
mass
tag
class
atomic
valence
name
story
atomicweightforeachatominthesystem
integeratomlabelsfrominputcoordinatesfile
atomclassnumberforeachatominthesystem
atomicnumberforeachatominthesystem
valencenumberforeachatominthesystem
atomnameforeachatominthesystem
descriptivetypeforeachatominsystem
ATOMS
number,positionandtypeofcurrentatoms
x
y
z
n
type
currentx-coordinateforeachatominthesystem
currenty-coordinateforeachatominthesystem
currentz-coordinateforeachatominthesystem
totalnumberofatomsinthecurrentsystem
atomtypenumberforeachatominthesystem
BATH
temperatureandpressurecontrolparameters
maxnose
kelvin0
kelvin
atmsph
tautemp
taupres
compress
collide
xnh
vnh
qnh
gnh
isothermal
isobaric
tempvary
thermostat
barostat
maximumlengthoftheNose-Hooverchain
targetvalueforthesystemtemperature(K)
variabletargettemperatureforthermostat(K)
targetvalueforthesystempressure(atm)
timeconstantforBerendsenthermostat(psec)
timeconstantforBerendsenbarostat(psec)
isothermalcompressibilityofmedium(atm-1)
collisionfrequencyforAndersenthermostat
positionofeachchainedNose-Hooverthermostat
velocityofeachchainedNose-Hooverthermostat
massforeachchainedNose-Hooverthermostat
couplingbetweenchainedNose-Hooverthermostats
logicalflaggoverninguseoftemperaturecontrol
logicalflaggoverninguseofpressurecontrol
logicalflagtoenablevariabletargetthermostat
choiceoftemperaturecontrolmethodtobeused
choiceofpressurecontrolmethodtobeused
BITOR
bitorsionswithinthecurrentstructure
nbitor
ibitor
totalnumberofbitorsionsinthesystem
numbersoftheatomsineachbitorsion
BNDPOT
specificsofbondstretchfunctionalforms
141
TINKERUser'sGuide
141
cbnd
qbnd
bndunit
bndtyp
cubiccoefficientinbondstretchpotential
quarticcoefficientinbondstretchpotential
convertbondstretchenergytokcal/mole
typeofbondstretchpotentialenergyfunction
BOND
covalentbondsinthecurrentstructure
bk
bl
nbond
ibnd
bondstretchforceconstants(kcal/mole/Ang**2)
idealbondlengthvaluesinAngstroms
totalnumberofbondstretchesinthesystem
numbersoftheatomsineachbondstretch
BORDER
bondordersforaconjugatedpisystem
pbpl
pnpl
pi-bondordersforbondsin"planar"pisystem
pi-bondordersforbondsin"nonplanar"pisystem
BOUND
controlofperiodicboundaryconditions
polycut
polycut2
use_bounds
use_image
use_replica
use_polymer
cutoffdistanceforinfinitepolymernonbonds
squareofinfinitepolymernonbondcutoff
flagtouseperiodicboundaryconditions
flagtouseimagesforperiodicsystem
flagtousereplicatesforperiodicsystem
flagtomarkpresenceofinfinitepolymer
BOXES
parametersforperiodicboundaryconditions
xbox
ybox
zbox
alpha
beta
gamma
xbox2
ybox2
zbox2
box34
recip
volbox
beta_sin
beta_cos
gamma_sin
gamma_cos
beta_term
gamma_term
orthogonal
monoclinic
triclinic
octahedron
spacegrp
lengthinAngsofa-axisofperiodicbox
lengthinAngsofb-axisofperiodicbox
lengthinAngsofc-axisofperiodicbox
angleindegreesbetweenb-andc-axesofbox
angleindegreesbetweena-andc-axesofbox
angleindegreesbetweena-andb-axesofbox
halfofthea-axislengthofperiodicbox
halfoftheb-axislengthofperiodicbox
halfofthec-axislengthofperiodicbox
three-fourthsaxislengthoftruncatedoctahedron
reciprocallatticevectorsasmatrixcolumns
volumeinAng**3oftheperiodicbox
sineofthebetaperiodicboxangle
cosineofthebetaperiodicboxangle
sineofthegammaperiodicboxangle
cosineofthegammaperiodicboxangle
termusedingeneratingtriclinicbox
termusedingeneratingtriclinicbox
flagtomarkperiodicboxasorthogonal
flagtomarkperiodicboxasmonoclinic
flagtomarkperiodicboxastriclinic
flagtomarkboxastruncatedoctahedron
spacegroupsymbolfortheunitcelltype
142
TINKERUser'sGuide
142
CELL
periodicboundariesusingreplicatedcells
xcell
ycell
zcell
xcell2
ycell2
zcell2
ncell
icell
lengthofthea-axisofthecompletereplicatedcell
lengthoftheb-axisofthecompletereplicatedcell
lengthofthec-axisofthecompletereplicatedcell
halfthelengthofthea-axisofthereplicatedcell
halfthelengthoftheb-axisofthereplicatedcell
halfthelengthofthec-axisofthereplicatedcell
totalnumberofcellreplicatesforperiodicboundaries
offsetalongaxesforeachreplicateperiodiccell
CHARGE
partialchargesforthecurrentstructure
pchg
nion
iion
jion
kion
chglist
magnitudeofthepartialcharges(e-)
totalnumberofpartialchargesinsystem
numberoftheatomsiteforeachpartialcharge
neighborgenerationsiteforeachpartialcharge
cutoffswitchingsiteforeachpartialcharge
partialchargesiteforeachatom(0=nocharge)
CHGPOT
specificsofcharge-chargefunctionalform
dielec
c2scale
c3scale
c4scale
c5scale
neutnbr
neutcut
dielectricconstantforelectrostaticinteractions
factorbywhich1-2chargeinteractionsarescaled
factorbywhich1-3chargeinteractionsarescaled
factorbywhich1-4chargeinteractionsarescaled
factorbywhich1-5chargeinteractionsarescaled
logicalflaggoverninguseofneutralgroupneighbors
logicalflaggoverninguseofneutralgroupcutoffs
CHRONO
timingstatisticsforthecurrentprogram
cputim
elapsedcputimeinsecondssincestartofprogram
COUPLE
near-neighboratomconnectivitylists
maxn13
maxn14
maxn15
n12
i12
n13
i13
n14
i14
n15
i15
maximumnumberofatoms1-3connectedtoanatom
maximumnumberofatoms1-4connectedtoanatom
maximumnumberofatoms1-5connectedtoanatom
numberofatomsdirectlybondedtoeachatom
atomnumbersofatoms1-2connectedtoeachatom
numberofatomsina1-3relationtoeachatom
atomnumbersofatoms1-3connectedtoeachatom
numberofatomsina1-4relationtoeachatom
atomnumbersofatoms1-4connectedtoeachatom
numberofatomsina1-5relationtoeachatom
atomnumbersofatoms1-5connectedtoeachatom
CUTOFF
cutoffdistancesforenergyinteractions
143
TINKERUser'sGuide
143
vdwcut
chgcut
dplcut
mpolecut
vdwtaper
chgtaper
dpltaper
mpoletaper
ewaldcut
use_ewald
use_lights
cutoffdistanceforvanderWaalsinteractions
cutoffdistanceforcharge-chargeinteractions
cutoffdistancefordipole-dipoleinteractions
cutoffdistanceforatomicmultipoleinteractions
distanceatwhichvanderWaalsswitchingbegins
distanceatwhichcharge-chargeswitchingbegins
distanceatwhichdipole-dipoleswitchingbegins
distanceatwhichatomicmultipoleswitchingbegins
cutoffdistancefordirectspaceEwaldsummation
logicalflaggoverninguseofEwaldsummationterm
logicalflagtousemethodoflightsneighbors
DERIV
Cartesiancoordinatederivativecomponents
desum
deb
dea
deba
deub
deaa
deopb
deopd
deid
deit
det
dept
debt
dett
dev
dec
decd
ded
dem
dep
der
des
delf
deg
dex
totalenergyCartesiancoordinatederivatives
bondstretchCartesiancoordinatederivatives
anglebendCartesiancoordinatederivatives
stretch-bendCartesiancoordinatederivatives
Urey-BradleyCartesiancoordinatederivatives
angle-angleCartesiancoordinatederivatives
out-of-planebendCartesiancoordinatederivatives
out-of-planedistanceCartesiancoordinatederivatives
improperdihedralCartesiancoordinatederivatives
impropertorsionCartesiancoordinatederivatives
torsionalCartesiancoordinatederivatives
pi-orbitaltorsionCartesiancoordinatederivatives
stretch-torsionCartesiancoordinatederivatives
torsion-torsionCartesiancoordinatederivatives
vanderWaalsCartesiancoordinatederivatives
charge-chargeCartesiancoordinatederivatives
charge-dipoleCartesiancoordinatederivatives
dipole-dipoleCartesiancoordinatederivatives
multipoleCartesiancoordinatederivatives
polarizationCartesiancoordinatederivatives
reactionfieldCartesiancoordinatederivatives
solvationCartesiancoordinatederivatives
metalligandfieldCartesiancoordinatederivatives
geometricrestraintCartesiancoordinatederivatives
extraenergytermCartesiancoordinatederivatives
DIPOLE
atom&bonddipolesforcurrentstructure
bdpl
sdpl
ndipole
idpl
magnitudeofeachofthedipoles(Debyes)
positionofeachdipolebetweendefiningatoms
totalnumberofdipolesinthesystem
numbersofatomsthatdefineeachdipole
DISGEO
distancegeometryboundsandparameters
bnd
vdwrad
vdwmax
distancegeometryupperandlowerboundsmatrix
hardsphereradiifordistancegeometryatoms
maximumvalueofhardspheresumforanatompair
144
TINKERUser'sGuide
144
compact
pathmax
use_invert
use_anneal
indexoflocaldistancecompactiononembedding
maximumvalueofupperboundaftersmoothing
flagtouseenantiomerclosesttoinputstructure
flagtousesimulatedannealingrefinement
DOMEGA
derivativecomponentsovertorsions
tesum
teb
tea
teba
teub
teaa
teopb
teopd
teid
teit
tet
tept
tebt
tett
tev
tec
tecd
ted
tem
tep
ter
tes
telf
teg
tex
totalenergyderivativesovertorsions
bondstretchderivativesovertorsions
anglebendderivativesovertorsions
stretch-bendderivativesovertorsions
Urey-Bradleyderivativesovertorsions
angle-anglederivativesovertorsions
out-of-planebendderivativesovertorsions
out-of-planedistancederivativesovertorsions
improperdihedralderivativesovertorsions
impropertorsionderivativesovertorsions
torsionalderivativesovertorsions
pi-orbitaltorsionderivativesovertorsions
stretch-torsionderivativesovertorsions
torsion-torsionderivativesovertorsions
vanderWaalsderivativesovertorsions
charge-chargederivativesovertorsions
charge-dipolederivativesovertorsions
dipole-dipolederivativesovertorsions
atomicmultipolederivativesovertorsions
polarizationderivativesovertorsions
reactionfieldderivativesovertorsions
solvationderivativesovertorsions
metalligandfieldderivativesovertorsions
geometricrestraintderivativesovertorsions
extraenergytermderivativesovertorsions
ENERGI
individualpotentialenergycomponents
esum
eb
ea
eba
eub
eaa
eopb
eopd
eid
eit
et
ept
ebt
ett
ev
ec
ecd
ed
totalpotentialenergyofthesystem
bondstretchpotentialenergyofthesystem
anglebendpotentialenergyofthesystem
stretch-bendpotentialenergyofthesystem
Urey-Bradleypotentialenergyofthesystem
angle-anglepotentialenergyofthesystem
out-of-planebendpotentialenergyofthesystem
out-of-planedistancepotentialenergyofthesystem
improperdihedralpotentialenergyofthesystem
impropertorsionpotentialenergyofthesystem
torsionalpotentialenergyofthesystem
pi-orbitaltorsionpotentialenergyofthesystem
stretch-torsionpotentialenergyofthesystem
torsion-torsionpotentialenergyofthesystem
vanderWaalspotentialenergyofthesystem
charge-chargepotentialenergyofthesystem
charge-dipolepotentialenergyofthesystem
dipole-dipolepotentialenergyofthesystem
145
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145
em
ep
er
es
elf
eg
ex
atomicmultipolepotentialenergyofthesystem
polarizationpotentialenergyofthesystem
reactionfieldpotentialenergyofthesystem
solvationpotentialenergyofthesystem
metalligandfieldpotentialenergyofthesystem
geometricrestraintpotentialenergyofthesystem
extratermpotentialenergyofthesystem
EWALD
parametersforregularorPMEwaldsummation
aewald
frecip
tinfoil
Ewaldconvergencecoefficientvalue(Ang-1)
fractionalcutoffvalueforreciprocalsphere
flaggoverninguseoftinfoilboundaryconditions
EWREG
exponentialfactorsforregularEwaldsum
maxvec
ejc
ejs
ekc
eks
elc
els
maximumnumberofk-vectorsperreciprocalaxis
exponentalfactorsforcosinealongthej-axis
exponentalfactorsforsinealongthej-axis
exponentalfactorsforcosinealongthek-axis
exponentalfactorsforsinealongthek-axis
exponentalfactorsforcosinealongthel-axis
exponentalfactorsforsinealongthel-axis
FACES
variablesforConnollyareaandvolume
maxnbr
maxtt
maxt
maxp
maxv
maxen
maxfn
maxc
maxep
maxfs
maxcy
mxcyep
maxfp
mxfpcy
maximumnumberofneighboringatompairs
maximumnumberoftemporarytori
maximumnumberoftotaltori
maximumnumberofprobepositions
maximumnumberofvertices
maximumnumberofconcaveedges
maximumnumberofconcavefaces
maximumnumberofcircles
maximumnumberofconvexedges
maximumnumberofsaddlefaces
maximumnumberofcycles
maximumnumberofcycleconvexedges
maximumnumberofconvexfaces
maximumnumberofconvexfacecycles
FIELDS
molecularmechanicsforcefielddescription
biotyp
forcefield
forcefieldatomtypeofeachbiopolymertype
stringusedtodescribethecurrentforcefield
FILES
nameandnumberofcurrentstructurefiles
nprior
ldir
leng
numberofpreviouslyexistingcyclefiles
lengthincharactersofthedirectoryname
lengthincharactersofthebasefilename
146
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146
filename
outfile
basefilenameusedbydefaultforallfiles
outputfilenameusedforintermediateresults
FRACS
atomdistancestomolecularcenterofmass
xfrac
yfrac
zfrac
fractionalcoordinatealonga-axisofcenterofmass
fractionalcoordinatealongb-axisofcenterofmass
fractionalcoordinatealongc-axisofcenterofmass
GROUP
partitioningofsystemintoatomgroups
grpmass
wgrp
ngrp
kgrp
igrp
grplist
use_group
use_intra
use_inter
totalmassofalltheatomsineachgroup
weightforeachsetofgroup-groupinteractions
totalnumberofatomgroupsinthesystem
contiguouslistoftheatomsineachgroup
firstandlastatomofeachgroupinthelist
numberofthegrouptowhicheachatombelongs
flagtousepartitioningofsystemintogroups
flagtoincludeonlyintragroupinteractions
flagtoincludeonlyintergroupinteractions
HESCUT
cutoffvalueforHessianmatrixelements
hesscut
magnitudeofsmallestallowedHessianelement
HESSN
CartesianHessianelementsforasingleatom
hessx
hessy
hessz
Hessianelementsforx-componentofcurrentatom
Hessianelementsfory-componentofcurrentatom
Hessianelementsforz-componentofcurrentatom
IMPROP
improperdihedralsinthecurrentstructure
kprop
vprop
niprop
iiprop
forceconstantvaluesforimproperdihedralangles
idealimproperdihedralanglevalueindegrees
totalnumberofimproperdihedralanglesinthesystem
numbersoftheatomsineachimproperdihedralangle
IMPTOR
impropertorsionsinthecurrentstructure
itors1
itors2
itors3
nitors
iitors
1-foldamplitudeandphaseforeachimpropertorsion
2-foldamplitudeandphaseforeachimpropertorsion
3-foldamplitudeandphaseforeachimpropertorsion
totalnumberofimpropertorsionalanglesinthesystem
numbersoftheatomsineachimpropertorsionalangle
INFORM
controlvaluesforI/Oandprogramflow
digits
iprint
iwrite
decimalplacesoutputforenergyandcoordinates
stepsbetweenstatusprinting(0=noprinting)
stepsbetweencoordinatedumps(0=nodumps)
147
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147
isend
verbose
debug
holdup
abort
stepsbetweensocketcommunication(0=nosockets)
logicalflagtoturnonextrainformation
logicalflagtoturnonfulldebugprinting
logicalflagtowaitforcarriagereturnonexit
logicalflagtostopexecutionatnextchance
INTER
sumofintermolecularenergycomponents
einter
totalintermolecularpotentialenergy
IOUNIT
Fortraninput/output(I/O)unitnumbers
iout
input
FortranI/Ounitformajoroutput(default=6)
FortranI/Ounitformajorinput(default=5)
KANANG
forcefieldparametersforangle-angleterms
anan
angle-anglecrosstermparametersforeachatomclass
KANGS
forcefieldparametersforbondanglebending
maxna
maxna5
maxna4
maxna3
maxnaf
acon
acon5
acon4
acon3
aconf
ang
ang5
ang4
ang3
angf
ka
ka5
ka4
ka3
kaf
maximumnumberofharmonicanglebendparameterentries
maximumnumberof5-memberedringanglebendentries
maximumnumberof4-memberedringanglebendentries
maximumnumberof3-memberedringanglebendentries
maximumnumberofFourieranglebendparameterentries
forceconstantparametersforharmonicanglebends
forceconstantparametersfor5-ringanglebends
forceconstantparametersfor4-ringanglebends
forceconstantparametersfor3-ringanglebends
forceconstantparametersforFourieranglebends
bondangleparametersforharmonicanglebends
bondangleparametersfor5-ringanglebends
bondangleparametersfor4-ringanglebends
bondangleparametersfor3-ringanglebends
phaseshiftangleandperiodicityforFourierbends
stringofatomclassesforharmonicanglebends
stringofatomclassesfor5-ringanglebends
stringofatomclassesfor4-ringanglebends
stringofatomclassesfor3-ringanglebends
stringofatomclassesforFourieranglebends
KATOMS
forcefieldparametersfortheatomtypes
weight
atmcls
atmnum
ligand
symbol
describe
averageatomicmassofeachatomtype
atomclassnumberforeachoftheatomtypes
atomicnumberforeachoftheatomtypes
numberofatomstobeattachedtoeachatomtype
modifiedatomicsymbolforeachatomtype
stringidentifingeachoftheatomtypes
148
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148
KBONDS
forcefieldparametersforbondstretching
maxnb
maxnb5
maxnb4
maxnb3
maxnel
bcon
bcon5
bcon4
bcon3
blen
blen5
blen4
blen3
dlen
kb
kb5
kb4
kb3
kel
maximumnumberofbondstretchparameterentries
maximumnumberof5-memberedringbondstretchentries
maximumnumberof4-memberedringbondstretchentries
maximumnumberof3-memberedringbondstretchentries
maximumnumberofelectronegativitybondcorrections
forceconstantparametersforharmonicbondstretch
forceconstantparametersfor5-ringbondstretch
forceconstantparametersfor4-ringbondstretch
forceconstantparametersfor3-ringbondstretch
bondlengthparametersforharmonicbondstretch
bondlengthparametersfor5-ringbondstretch
bondlengthparametersfor4-ringbondstretch
bondlengthparametersfor3-ringbondstretch
electronegativitybondlengthcorrectionparameters
stringofatomclassesforharmonicbondstretch
stringofatomclassesfor5-ringbondstretch
stringofatomclassesfor4-ringbondstretch
stringofatomclassesfor3-ringbondstretch
stringofatomclassesforelectronegativitycorrections
KCHRGE
forcefieldparametersforpartialcharges
chg
partialchargeparametersforeachatomtype
KDIPOL
forcefieldparametersforbonddipoles
maxnd
maxnd5
maxnd4
maxnd3
dpl
dpl5
dpl4
dpl3
pos
pos5
pos4
pos3
kd
kd5
kd4
kd3
maximumnumberofbonddipoleparameterentries
maximumnumberof5-memberedringdipoleentries
maximumnumberof4-memberedringdipoleentries
maximumnumberof3-memberedringdipoleentries
dipolemomentparametersforbonddipoles
dipolemomentparametersfor5-ringdipoles
dipolemomentparametersfor4-ringdipoles
dipolemomentparametersfor3-ringdipoles
dipolepositionparametersforbonddipoles
dipolepositionparametersfor5-ringdipoles
dipolepositionparametersfor4-ringdipoles
dipolepositionparametersfor3-ringdipoles
stringofatomclassesforbonddipoles
stringofatomclassesfor5-ringdipoles
stringofatomclassesfor4-ringdipoles
stringofatomclassesfor3-ringdipoles
KEYS
contentsofcurrentkeywordparameterfile
nkey
keyline
numberofnonblanklinesinthekeywordfile
contentsofeachindividualkeywordfileline
KGEOMS
parametersforthegeometricalrestraints
149
TINKERUser'sGuide
149
xpfix
ypfix
zpfix
pfix
dfix
afix
tfix
gfix
chir
depth
width
rwall
npfix
ipfix
kpfix
ndfix
idfix
nafix
iafix
ntfix
itfix
ngfix
igfix
nchir
ichir
use_basin
use_wall
x-coordinatetargetforeachrestrainedposition
y-coordinatetargetforeachrestrainedposition
z-coordinatetargetforeachrestrainedposition
forceconstantandflat-wellrangeforeachposition
forceconstantandtargetrangeforeachdistance
forceconstantandtargetrangeforeachangle
forceconstantandtargetrangeforeachtorsion
forceconstantandtargetrangeforeachgroupdistance
forceconstantandtargetrangeforchiralcenters
depthofshallowGaussianbasinrestraint
exponentialwidthcoefficientofGaussianbasin
radiusofsphericaldropletboundaryrestraint
numberofpositionrestraintstobeapplied
atomnumberinvolvedineachpositionrestraint
flagstousex-,y-,z-coordinatepositionrestraints
numberofdistancerestraintstobeapplied
atomnumbersdefiningeachdistancerestraint
numberofanglerestraintstobeapplied
atomnumbersdefiningeachanglerestraint
numberoftorsionalrestraintstobeapplied
atomnumbersdefiningeachtorsionalrestraint
numberofgroupdistancerestraintstobeapplied
groupnumbersdefiningeachgroupdistancerestraint
numberofchiralityrestraintstobeapplied
atomnumbersdefiningeachchiralityrestraint
logicalflaggoverninguseofGaussianbasin
logicalflaggoverninguseofdropletboundary
KHBOND
forcefieldparametersforH-bondingterms
maxnhb
radhb
epshb
khb
maximumnumberofhydrogenbondingpairentries
radiusparameterforhydrogenbondingpairs
welldepthparameterforhydrogenbondingpairs
stringofatomtypesforhydrogenbondingpairs
KIPROP
forcefieldparametersforimproperdihedral
maxndi
dcon
tdi
kdi
maximumnumberofimproperdihedralparameterentries
forceconstantparametersforimproperdihedrals
idealdihedralanglevaluesforimproperdihedrals
stringofatomclassesforimproperdihedralangles
KITORS
forcefieldparametersforimpropertorsions
maxnti
ti1
ti2
ti3
kti
maximumnumberofimpropertorsionparameterentries
torsionalparametersforimproper1-foldrotation
torsionalparametersforimproper2-foldrotation
torsionalparametersforimproper3-foldrotation
stringofatomclassesforimpropertorsionalparameters
KMULTI
forcefieldparametersforatomicmultipoles
150
TINKERUser'sGuide
150
maxnmp
multip
mpaxis
kmp
maximumnumberofatomicmultipoleparameterentries
atomicmonopole,dipoleandquadrupolevalues
typeoflocalaxisdefinitionforatomicmultipoles
stringofatomtypesforatomicmultipoles
KOPBND
forcefieldparametersforout-of-planebend
maxnopb
copb
kaopb
maximumnumberofout-of-planebendingentries
forceconstantparametersforout-of-planebending
stringofatomclassesforout-of-planebending
KOPDST
forcefieldparametersforout-planedistance
maxnopb
copb
kaopb
maximumnumberofout-of-planedistanceentries
forceconstantparametersforout-of-planedistance
stringofatomclassesforout-of-planedistance
KORBS
forcefieldparametersforpisystemorbitals
maxnpi
electron
ionize
repulse
sslope
tslope
kpi
maximumnumberofpisystembondparameterentries
numberofpi-electronsforeachatomclass
ionizationpotentialforeachatomclass
repulsionintegralvalueforeachatomclass
slopeforbondstretchvs.pi-bondorder
slopefor2-foldtorsionvs.pi-bondorder
stringofatomclassesforpisystembonds
KPITOR
forcefieldparametersforpi-orbittorsions
maxnpt
ptcon
kpt
maximumnumberofpi-orbitaltorsionparameterentries
forceconstantparametersforpi-orbitaltorsions
stringofatomclassesforpi-orbitaltorsionterms
KPOLR
forcefieldparametersforpolarizability
polr
pgrp
dipolepolarizabilityparametersforeachatomtype
connectedtypesinpolarizationgroupofeachatomtype
KSTBND
forcefieldparametersforstretch-bending
stbn
stretch-bendingparametersforeachatomclass
KSTTOR
forcefieldparametersforstretch-torsions
maxnbt
btcon
kbt
maximumnumberofstretch-torsionparameterentries
forceconstantparametersforstretch-torsion
stringofatomclassesforbondsinstretch-torsion
KTORSN
forcefieldparametersfortorsionalangles
151
TINKERUser'sGuide
151
maxnt
maxnt5
maxnt4
t1
t2
t3
t4
t5
t6
t15
t25
t35
t45
t55
t65
t14
t24
t34
t44
t54
t64
kt
kt5
kt4
maximumnumberoftorsionalangleparameterentries
maximumnumberof5-memberedringtorsionentries
maximumnumberof4-memberedringtorsionentries
torsionalparametersforstandard1-foldrotation
torsionalparametersforstandard2-foldrotation
torsionalparametersforstandard3-foldrotation
torsionalparametersforstandard4-foldrotation
torsionalparametersforstandard5-foldrotation
torsionalparametersforstandard6-foldrotation
torsionalparametersfor1-foldrotationin5-ring
torsionalparametersfor2-foldrotationin5-ring
torsionalparametersfor3-foldrotationin5-ring
torsionalparametersfor4-foldrotationin5-ring
torsionalparametersfor5-foldrotationin5-ring
torsionalparametersfor6-foldrotationin5-ring
torsionalparametersfor1-foldrotationin4-ring
torsionalparametersfor2-foldrotationin4-ring
torsionalparametersfor3-foldrotationin4-ring
torsionalparametersfor4-foldrotationin4-ring
torsionalparametersfor5-foldrotationin4-ring
torsionalparametersfor6-foldrotationin4-ring
stringofatomclassesfortorsionalangles
stringofatomclassesfor5-ringtorsions
stringofatomclassesfor4-ringtorsions
KTRTOR
forcefieldparametersfortorsion-torsions
maxntt
maxtgrd
maxtgrd2
ttx
tty
tbf
tbx
tby
tbxy
tnx
tny
ktt
maximumnumberoftorsion-torsionparameterentries
maximumdimensionoftorsion-torsionsplinegrid
maximumnumberoftorsion-torsionsplinegridpoints
anglevaluesforfirsttorsionofsplinegrid
anglevaluesforsecondtorsionofsplinegrid
functionvaluesatpointsonsplinegrid
gradientoverfirsttorsionofsplinegrid
gradientoversecondtorsionofsplinegrid
Hessiancrosscomponentsoversplinegrid
numberofcolumnsintorsion-torsionsplinegrid
numberofrowsintorsion-torsionsplinegrid
stringoftorsion-torsionatomclasses
KURYBR
forcefieldparametersforUrey-Bradleyterms
maxnu
ucon
dst13
ku
maximumnumberofUrey-Bradleyparameterentries
forceconstantparametersforUrey-Bradleyterms
ideal1-3distanceparametersforUrey-Bradleyterms
stringofatomclassesforUrey-Bradleyterms
KVDWPR
forcefieldparametersforspecialvdwterms
maxnvp
radpr
epspr
maximumnumberofspecialvanderWaalspairentries
radiusparameterforspecialvanderWaalspairs
welldepthparameterforspecialvanderWaalspairs
152
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152
kvpr
stringofatomclassesforspecialvanderWaalspairs
KVDWS
forcefieldparametersforvanderWaalsterms
rad
eps
rad4
eps4
reduct
vanderWaalsradiusparameterforeachatomclass
vanderWaalswelldepthparameterforeachatomclass
vanderWaalsradiusparameterin1-4interactions
vanderWaalswelldepthparameterin1-4interactions
vanderWaalsreductionfactorforeachatomclass
LIGHT
indicesformethodoflightspairneighbors
nlight
kbx
kby
kbz
kex
key
kez
locx
locy
locz
rgx
rgy
rgz
totalnumberofsitesformethodoflightscalculation
lowindexofneighborsofeachsiteinthex-sortedlist
lowindexofneighborsofeachsiteinthey-sortedlist
lowindexofneighborsofeachsiteinthez-sortedlist
highindexofneighborsofeachsiteinthex-sortedlist
highindexofneighborsofeachsiteinthey-sortedlist
highindexofneighborsofeachsiteinthez-sortedlist
pointerfromx-sortedlistintooriginalinteractionlist
pointerfromy-sortedlistintooriginalinteractionlist
pointerfromz-sortedlistintooriginalinteractionlist
pointerfromoriginalinteractionlistintox-sortedlist
pointerfromoriginalinteractionlistintoy-sortedlist
pointerfromoriginalinteractionlistintoz-sortedlist
LINMIN
parametersforlinesearchminimization
stpmin
stpmax
cappa
slpmax
angmax
intmax
minimumsteplengthincurrentlinesearchdirection
maximumsteplengthincurrentlinesearchdirection
stringencyoflinesearch(0=tight<cappa<1=loose)
projectedgradientabovewhichstepsizeisreduced
maximumanglebetweensearchdirectionand-gradient
maximumnumberofinterpolationsduringlinesearch
MATH
mathematicalandgeometricalconstants
radian
pi
sqrtpi
logten
sqrttwo
twosix
conversionfactorfromradianstodegrees
numericalvalueofthegeometricconstant
numericalvalueofthesquarerootofPi
numericalvalueofthenaturallogoften
numericalvalueofthesquarerootoftwo
numericalvalueofthesixthrootoftwo
MDSTUF
controlofmoleculardynamicstrajectory
nfree
velsave
frcsave
uindsave
integrate
totalnumberofdegreesoffreedomforasystem
flagtosavevelocityvectorcomponentstoafile
flagtosaveforcevectorcomponentstoafile
flagtosaveinducedatomicdipolestoafile
typeofmoleculardynamicsintegrationalgorithm
153
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153
MINIMA
generalparametersforminimizations
fctmin
hguess
maxiter
nextiter
valuebelowwhichfunctionisdeemedoptimized
initialvaluefortheH-matrixdiagonalelements
maximumnumberofiterationsduringoptimization
iterationnumbertouseforthefirstiteration
MOLCUL
individualmoleculeswithincurrentsystem
molmass
totmass
nmol
kmol
imol
molcule
molecularweightforeachmoleculeinthesystem
totalweightofallthemoleculesinthesystem
totalnumberofseparatemoleculesinthesystem
contiguouslistoftheatomsineachmolecule
firstandlastatomofeachmoleculeinthelist
numberofthemoleculetowhicheachatombelongs
MOLDYN
velocityandaccelerationonMDtrajectory
v
a
aold
currentvelocityofeachatomalongthex,y,z-axes
currentaccelerationofeachatomalongx,y,z-axes
previousaccelerationofeachatomalongx,y,z-axes
MOMENT
componentsofelectricmultipolemoments
netchg
netdpl
netqdp
xdpl
ydpl
zdpl
xxqdp
xyqdp
xzqdp
yxqdp
yyqdp
yzqdp
zxqdp
zyqdp
zzqdp
netelectricchargeforthetotalsystem
dipolemomentmagnitudeforthetotalsystem
diagonalquadrupole(Qxx,Qyy,Qzz)forsystem
dipolevectorx-componentintheglobalframe
dipolevectory-componentintheglobalframe
dipolevectorz-componentintheglobalframe
quadrupoletensorxx-componentinglobalframe
quadrupoletensorxy-componentinglobalframe
quadrupoletensorxz-componentinglobalframe
quadrupoletensoryx-componentinglobalframe
quadrupoletensoryy-componentinglobalframe
quadrupoletensoryz-componentinglobalframe
quadrupoletensorzx-componentinglobalframe
quadrupoletensorzy-componentinglobalframe
quadrupoletensorzz-componentinglobalframe
MPLPOT
specificsofatomicmultipolefunctions
m2scale
m3scale
m4scale
m5scale
factorbywhich1-2multipoleinteractionsarescaled
factorbywhich1-3multipoleinteractionsarescaled
factorbywhich1-4multipoleinteractionsarescaled
factorbywhich1-5multipoleinteractionsarescaled
MPOLE
multipolecomponentsforcurrentstructure
maxpole
maxcomponents(monopole=1,dipole=4,quadrupole=13)
154
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154
pole
rpole
npole
ipole
polsiz
zaxis
xaxis
yaxis
polaxe
multipolevaluesforeachsiteinthelocalframe
multipolesrotatedtotheglobalcoordinatesystem
totalnumberofmultipolesitesinthesystem
numberoftheatomforeachmultipolesite
numberofmutipolecomponentsateachmultipolesite
numberofthez-axisdefiningatomforeachsite
numberofthex-axisdefiningatomforeachsite
numberofthey-axisdefiningatomforeachsite
localaxistypeforeachmultipolesite
MUTANT
hybridatomsforfreeenergyperturbation
lambda
nhybrid
ihybrid
type0
class0
type1
class1
alter
weightingofinitialstateinhybridHamiltonian
numberofatomsmutatedfrominitialtofinalstate
atomicsitesdifferingininitialandfinalstate
atomtypeofeachatomintheinitialstatesystem
atomclassofeachatomintheinitialstatesystem
atomtypeofeachatominthefinalstatesystem
atomclassofeachatominthefinalstatesystem
trueifanatomistobemutated,falseotherwise
NUCLEO
parametersfornucleicacidstructure
bkbone
glyco
pucker
dblhlx
deoxy
hlxform
phosphatebackboneanglesforeachnucleotide
glycosidictorsionalangleforeachnucleotide
sugarpucker,either2=2'-endoor3=3'-endo
flagtomarksystemasnucleicaciddoublehelix
flagtomarkdeoxyriboseorribosesugarunits
helixform(A,BorZ)ofpolynucleotidestrands
OMEGA
dihedralsfortorsionalspacecomputations
dihed
nomega
iomega
zline
currentvalueinradiansofeachdihedralangle
numberofdihedralanglesallowedtorotate
numbersoftwoatomsdefiningrotationaxis
linenumberinZ-matrixofeachdihedralangle
OPBEND
out-of-planebendsinthecurrentstructure
kopb
nopbend
iopb
forceconstantvaluesforout-of-planebending
totalnumberofout-of-planebendsinthesystem
bondanglenumbersusedinout-of-planebending
OPDIST
out-of-planedistancesincurrentstructure
kopd
nopdist
iopb
forceconstantvaluesforout-of-planedistance
totalnumberofout-of-planedistancesinthesystem
numbersoftheatomsineachout-of-planedistance
ORBITS
orbitalenergiesforconjugatedpisystem
155
TINKERUser'sGuide
155
q
w
em
nfill
numberofpi-electronscontributedbyeachatom
ionizationpotentialofeachpisystematom
repulsionintegralforeachpisystematom
numberoffilledpisystemmolecularorbitals
OUTPUT
controlofcoordinateoutputfileformat
archive
noversion
overwrite
cyclesave
coordtype
logicalflagtosavestructuresinanarchive
logicalflaggoverninguseoffilenameversions
logicalflagtooverwriteintermediatefilesinplace
logicalflagtomarkuseofnumberedcyclefiles
selectsCartesian,internal,rigidbodyornone
PARAMS
contentsofforcefieldparameterfile
nprm
prmline
numberofnonblanklinesintheparameterfile
contentsofeachindividualparameterfileline
PATHS
parametersforElberreactionpathmethod
p0
p1
pmid
pvect
pstep
pzet
pnorm
acoeff
gc
reactantCartesiancoordinatesasvariables
productCartesiancoordinatesasvariables
midpointbetweenthereactantandproduct
vectorconnectingthereactantandproduct
steppercyclealongreactant-productvector
currentprojectiononreactant-productvector
lengthofthereactant-productvector
transformationmatrix'A'fromElberpaper
gradientsofthepathconstraints
PDB
definitionofaProteinDataBankstructure
xpdb
ypdb
zpdb
npdb
resnum
npdb12
ipdb12
pdblist
pdbtyp
atmnam
resnam
x-coordinateofeachatomstoredinPDBformat
y-coordinateofeachatomstoredinPDBformat
z-coordinateofeachatomstoredinPDBformat
numberofatomsstoredinProteinDataBankformat
numberoftheresiduetowhicheachatombelongs
numberofatomsdirectlybondedtoeachCONECTatom
atomnumbersofatomsconnectedtoeachCONECTatom
listoftheProteinDataBankatomnumberofeachatom
ProteinDataBankrecordtypeassignedtoeachatom
ProteinDataBankatomnameassignedtoeachatom
ProteinDataBankresiduenameassignedtoeachatom
PHIPSI
phi-psi-omega-chianglesforaprotein
phi
psi
omega
chi
chiral
valueofthephiangleforeachaminoacidresidue
valueofthepsiangleforeachaminoacidresidue
valueoftheomegaangleforeachaminoacidresidue
valuesofthechianglesforeachaminoacidresidue
chiralityofeachaminoacidresidue(1=L,-1=D)
156
TINKERUser'sGuide
156
disulf
residuejoinedtoeachresidueviaadisulfidelink
PIORBS
conjugatedsysteminthecurrentstructure
norbit
iorbit
reorbit
piperp
nbpi
bpi
ntpi
tpi
listpi
totalnumberofpisystemorbitalsinthesystem
numbersoftheatomscontainingpisystemorbitals
numberofevaluationsbetweenorbitalupdates
atomsdefininganormalplanetoeachorbital
totalnumberofbondsaffectedbythepisystem
bondandpiatomnumbersforeachpisystembond
totalnumberoftorsionsaffectedbythepisystem
torsionandpibondnumbersforeachpisystemtorsion
atomlistindicatingwhethereachatomhasanorbital
PISTUF
bondsandtorsionsinthecurrentpisystem
bkpi
blpi
kslope
lslope
torsp2
bondstretchforceconstantsforpi-bondorderof1.0
idealbondlengthvaluesforapi-bondorderof1.0
rateofforceconstantdecreasewithbondorderdecrease
rateofbondlengthincreasewithabondorderdecrease
2-foldtorsionalenergybarrierforpi-bondorderof1.0
PITORS
pi-orbitaltorsionsinthecurrentstructure
kpit
npitors
ipit
2-foldpi-orbitaltorsionalforceconstants
totalnumberofpi-orbitaltorsionalinteractions
numbersoftheatomsineachpi-orbitaltorsion
PME
parametersforparticlemeshEwaldsummation
maxfft
maxorder
maxtable
maxgrid
bsmod1
bsmod2
bsmod3
table
nfft1
nfft2
nfft3
bsorder
maximumnumberofpointsalongeachFFTdirection
maximumorderoftheB-splineapproximation
maximumsizeoftheFFTtablearray
maximumdimensionofthePMEchargegridarray
B-splinemodulialongthea-axisdirection
B-splinemodulialongtheb-axisdirection
B-splinemodulialongthec-axisdirection
intermediatearrayusedbytheFFTcalculation
numberofgridpointsalongthea-axisdirection
numberofgridpointsalongtheb-axisdirection
numberofgridpointsalongthec-axisdirection
orderofthePMEB-splineapproximation
POLAR
polarizabilitiesandinduceddipolemoments
polarity
pdamp
uind
uinp
npolar
dipolepolarizabilityforeachmultipolesite(Ang**3)
valueofpolarizabilitydampingfactorforeachsite
induceddipolecomponentsateachmultipolesite
induceddipolesinfieldusedforenergyinteractions
totalnumberofpolarizablesitesinthesystem
157
TINKERUser'sGuide
157
POLGRP
polarizablesitegroupconnectivitylists
maxp11
maxp12
maxp13
maxp14
np11
ip11
np12
ip12
np13
ip13
np14
ip14
maximumnumberofatomsinapolarizationgroup
maximumnumberofatomsingroups1-2toanatom
maximumnumberofatomsingroups1-3toanatom
maximumnumberofatomsingroups1-4toanatom
numberofatomsinpolarizationgroupofeachatom
atomnumbersofatomsinsamegroupaseachatom
numberofatomsingroups1-2toeachatom
atomnumbersofatomsingroups1-2toeachatom
numberofatomsingroups1-3toeachatom
atomnumbersofatomsingroups1-3toeachatom
numberofatomsingroups1-4toeachatom
atomnumbersofatomsingroups1-4toeachatom
POLPOT
specificsofpolarizationfunctionalform
poleps
polsor
pgamma
p2scale
p3scale
p4scale
p5scale
d1scale
d2scale
d3scale
d4scale
u1scale
u2scale
u3scale
u4scale
poltyp
induceddipoleconvergencecriterion(rmsDebyes/atom)
induceddipoleSORconvergenceaccelerationfactor
prefactorinexponentialpolarizationdampingterm
field1-2scalefactorforenergyevaluations
field1-3scalefactorforenergyevaluations
field1-4scalefactorforenergyevaluations
field1-5scalefactorforenergyevaluations
fieldintra-groupscalefactorfordirectinduced
field1-2groupscalefactorfordirectinduced
field1-3groupscalefactorfordirectinduced
field1-4groupscalefactorfordirectinduced
fieldintra-groupscalefactorformutualinduced
field1-2groupscalefactorformutualinduced
field1-3groupscalefactorformutualinduced
field1-4groupscalefactorformutualinduced
typeofpolarizationpotential(directormutual)
POTENT
usageofeachpotentialenergycomponent
use_bond
use_angle
use_strbnd
use_urey
use_angang
use_opbend
use_opdist
use_improp
use_imptor
use_tors
use_pitors
use_strtor
use_tortor
use_vdw
use_charge
use_chgdpl
logicalflaggoverninguseofbondstretchpotential
logicalflaggoverninguseofanglebendpotential
logicalflaggoverninguseofstretch-bendpotential
logicalflaggoverninguseofUrey-Bradleypotential
logicalflaggoverninguseofangle-anglecrossterm
logicalflaggoverninguseofout-of-planebendterm
logicalflaggoverninguseofout-of-planedistance
logicalflaggoverninguseofimproperdihedralterm
logicalflaggoverninguseofimpropertorsionterm
logicalflaggoverninguseoftorsionalpotential
logicalflaggoverninguseofpi-orbitaltorsionterm
logicalflaggoverninguseofstretch-torsionterm
logicalflaggoverninguseoftorsion-torsionterm
logicalflaggoverninguseofvdwderWaalspotential
logicalflaggoverninguseofcharge-chargepotential
logicalflaggoverninguseofcharge-dipolepotential
158
TINKERUser'sGuide
158
use_dipole
use_mpole
use_polar
use_rxnfld
use_solv
use_gbsa
use_metal
use_geom
use_extra
use_orbit
logicalflaggoverninguseofdipole-dipolepotential
logicalflaggoverninguseofmultipolepotential
logicalflaggoverninguseofpolarizationterm
logicalflaggoverninguseofreactionfieldterm
logicalflaggoverninguseofsurfaceareasolvation
logicalflaggoverninguseofGB/SAsolvationterm
logicalflaggoverninguseofligandfieldterm
logicalflaggoverninguseofgeometricrestraints
logicalflaggoverninguseofextrapotentialterm
logicalflaggoverninguseofpisystemcomputation
PRECIS
valuesofmachineprecisiontolerances
tiny
small
huge
thesmallestpositivefloatingpointvalue
thesmallestrelativefloatingpointspacing
thelargestrelativefloatingpointspacing
REFER
storageofreferenceatomiccoordinateset
xref
yref
zref
nref
reftyp
n12ref
i12ref
refleng
refltitle
refnam
reffile
reftitle
referencex-coordinateforeachatominthesystem
referencey-coordinateforeachatominthesystem
referencez-coordinateforeachatominthesystem
totalnumberofatomsinthereferencesystem
atomtypeforeachatominthereferencesystem
numberofatomsbondedtoeachreferenceatom
atomnumbersofatoms1-2connectedtoeachatom
lengthincharactersofthereferencefilename
lengthincharactersofthereferencetitlestring
atomnameforeachatominthereferencesystem
basefilenameforthereferencestructure
titleusedtodescribethereferencestructure
RESDUE
standardbiopolymerresidueabbreviations
amino
nuclz
amino1
nuclz1
three-letterabbreviationsforaminoacidstypes
three-letterabbreviationsfornucleicacidstypes
one-letterabbreviationsforaminoacidstypes
one-letterabbreviationsfornucleicacidstypes
RGDDYN
velocitiesandmomentaforrigidbodyMD
vcm
wcm
lm
linear
currenttranslationalvelocityofeachrigidbody
currentangularvelocityofeachrigidbody
currentangularmomentumofeachrigidbody
logicalflagtomarkgroupaslinearornonlinear
RIGID
rigidbodycoordinatesforatomgroups
xrb
yrb
zrb
rigidbodyreferencex-coordinateforeachatom
rigidbodyreferencey-coordinateforeachatom
rigidbodyreferencez-coordinateforeachatom
159
TINKERUser'sGuide
159
rbc
use_rigid
currentrigidbodycoordinatesforeachgroup
flagtomarkuseofrigidbodycoordinatesystem
RING
numberandlocationofsmallringstructures
nring3
iring3
nring4
iring4
nring5
iring5
nring6
iring6
totalnumberof3-memberedringsinthesystem
numbersoftheatomsinvolvedineach3-ring
totalnumberof4-memberedringsinthesystem
numbersoftheatomsinvolvedineach4-ring
totalnumberof5-memberedringsinthesystem
numbersoftheatomsinvolvedineach5-ring
totalnumberof6-memberedringsinthesystem
numbersoftheatomsinvolvedineach6-ring
ROTATE
moleculepartitionsforrotationofabond
nrot
rot
use_short
totalnumberofatomsmovingwhenbondrotates
atomnumbersofatomsmovingwhenbondrotates
logicalflaggoverninguseofshortestatomlist
RXNFLD
reactionfieldmatrixelementsandindices
b1
b2
ijk
firstreactionfieldmatrixelementarray
secondreactionfieldmatrixelementarray
indicesintothereactionfieldelementarrays
RXNPOT
specificsofreactionfieldfunctionalform
rfsize
rfbulkd
rfterms
radiusofreactionfieldspherecenteredatorigin
bulkdielectricconstantofreactionfieldcontinuum
numberoftermstouseinreactionfieldsummation
SCALES
parameterscalefactorsforoptimization
scale
set_scale
multiplicativefactorforeachoptimizationparameter
logicalflagtoshowifscalefactorshavebeenset
SEQUEN
sequenceinformationforabiopolymer
nseq
nchain
ichain
seqtyp
seq
chnnam
totalnumberofresiduesinbiopolymersequences
numberofseparatebiopolymersequencechains
firstandlastresidueineachbiopolymerchain
residuetypeforeachresidueinthesequence
three-lettercodeforeachresidueinthesequence
one-letteridentifierforeachsequencechain
SHAKE
definitionofShake/Rattleconstraints
krat
nrat
nratx
idealdistancevalueforrattleconstraint
numberofrattledistanceconstraintstoapply
numberofatomgroupspatialconstraintstoapply
160
TINKERUser'sGuide
160
irat
iratx
kratx
ratimage
use_rattle
atomnumbersofatomsinarattleconstraint
groupnumberofgroupinaspatialconstraint
spatialconstrainttype(1=plane,2=line,3=point)
flagtouseminimumimageforrattleconstraint
logicalflagtosetuseofrattlecontraints
SHUNT
polynomialswitchingfunctioncoefficients
off
off2
cut
cut2
c0
c1
c2
c3
c4
c5
f0
f1
f2
f3
f4
f5
f6
f7
distanceatwhichthepotentialenergygoestozero
squareofdistanceatwhichthepotentialgoestozero
distanceatwhichswitchingofthepotentialbegins
squareofdistanceatwhichtheswitchingbegins
zerothordercoefficientofmultiplicativeswitch
firstordercoefficientofmultiplicativeswitch
secondordercoefficientofmultiplicativeswitch
thirdordercoefficientofmultiplicativeswitch
fourthordercoefficientofmultiplicativeswitch
fifthordercoefficientofmultiplicativeswitch
zerothordercoefficientofadditiveswitchfunction
firstordercoefficientofadditiveswitchfunction
secondordercoefficientofadditiveswitchfunction
thirdordercoefficientofadditiveswitchfunction
fourthordercoefficientofadditiveswitchfunction
fifthordercoefficientofadditiveswitchfunction
sixthordercoefficientofadditiveswitchfunction
seventhordercoefficientofadditiveswitchfunction
SIZES
parametervaluestosetarraydimensions
"sizes.i"setsvaluesforcriticalarraydimensionsusedthroughoutthesoftware;theseparameterswill
fixthesizeofthelargestsystemsthatcanbehandled;valuestoolargefor thecomputer'smemory
and/orswapspacetoaccomodatewillresultinpoorperformanceoroutrightfailure
parameter:
maximumallowednumberof:
maxatm
maxval
maxgrp
maxtyp
maxclass
maxprm
maxkey
maxrot
maxvar
maxopt
maxhess
maxlight
maxvib
maxgeo
maxcell
maxring
maxfix
atomsinthemolecularsystem
atomsdirectlybondedtoanatom
user-definedgroupsofatoms
forcefieldatomtypedefinitions
forcefieldatomclassdefinitions
linesintheparameterfile
linesinthekeywordfile
bondsfortorsionalrotation
optimizationvariables(vectorstorage)
optimizationvariables(matrixstorage)
off-diagonalHessianelements
sitesformethodoflightsneighbors
vibrationalfrequencies
distancegeometrypoints
unitcellsinreplicatedcrystal
3-,4-,or5-memberedrings
geometricconstraintsandrestraints
161
TINKERUser'sGuide
161
maxbio
maxres
maxamino
maxnuc
maxbnd
maxang
maxtors
maxbitor
maxpi
maxpib
maxpit
biopolymeratomdefinitions
residuesinthemacromolecule
aminoacidresiduetypes
nucleicacidresiduetypes
covalentbondsinmolecularsystem
bondanglesinmolecularsystem
torsionalanglesinmolecularsystem
bitorsionsinmolecularsystem
atomsinconjugatedpisystem
covalentbondsinvolvingpisystem
torsionalanglesinvolvingpisystem
SOCKET
controlparametersforsocketcommunication
runtyp
cstep
cdt
cenergy
cdx
cdy
cdz
skt_init
use_socket
use_gui
closing
calculationtypeforpassingsocketinformation
currentoptimizationordynamicsstepnumber
currentdynamicscumulativesimulationtime
currentpotentialenergyfromsimulation
currentgradientcomponentsalongthex-axis
currentgradientcomponentsalongthey-axis
currentgradientcomponentsalongthez-axis
logicalflagsettotrueaftersocketinitialization
logicalflaggoverninguseofexternalsockets
logicalflagtoshowTINKERwasinvokedfromGUI
logicalflagtoindicateJVMandservershutdown
SOLUTE
parametersforcontinuumsolvationmodels
rsolv
vsolv
asolv
rborn
drb
doffset
p1
p2
p3
p4
p5
gpol
shct
wace
s2ace
uace
solvtyp
atomicradiusofeachatomforcontinuumsolvation
atomicvolumeofeachatomforcontinuumsolvation
atomicsolvationparameters(kcal/mole/Ang**2)
BornradiusofeachatomforGB/SAsolvation
solvationderivativeswithrespecttoBornradii
dielectricoffsettocontinuumsolvationatomicradii
single-atomscalefactorforanalyticalStillGB/SA
1-2interactionscalefactorforanalyticalStillGB/SA
1-3interactionscalefactorforanalyticalStillGB/SA
nonbondedscalefactorforanalyticalStillGB/SA
softcutoffparameterforanalyticalStillGB/SA
polarizationself-energyvaluesforeachatom
overlapscalingfactorsforHawkins-Cramer-TruhlarGB/SA
"omega"valuesforatomclasspairsforusewithACE
"sigma^2"valuesforatomclasspairsforusewithACE
"mu"valuesforatomclasspairsforusewithACE
solvationmodel(ASP,SASA,ONION,STILL,HCT,ACE)
STODYN
frictionalcoefficientsforSDtrajectory
friction
gamma
use_sdarea
globalfrictionalcoefficientforexposedparticle
atomicfrictionalcoefficientsforeachatom
logicalflagtousesurfaceareafrictionscaling
162
TINKERUser'sGuide
162
STRBND
stretch-bendsinthecurrentstructure
ksb
nstrbnd
isb
forceconstantforstretch-bendterms
totalnumberofstretch-bendinteractions
angleandbondnumbersusedinstretch-bend
STRTOR
stretch-torsionsinthecurrentstructure
kst
nstrtor
ist
1-,2-and3-foldstretch-torsionforceconstants
totalnumberofstretch-torsioninteractions
torsionandbondnumbersusedinstretch-torsion
SYNTRN
definitionofsynchronoustransitpath
t
pm
xmin1
xmin2
xm
valueofthepathcoordinate(0=reactant,1=product)
pathcoordinateforextrapointinquadratictransit
reactantcoordinatesasarrayofoptimizationvariables
productcoordinatesasarrayofoptimizationvariables
extracoordinatesetforquadraticsynchronoustransit
TITLES
titleforthecurrentmolecularsystem
ltitle
title
lengthincharactersofthenonblanktitlestring
titleusedtodescribethecurrentstructure
TORPOT
specificsoftorsionalfunctionalforms
idihunit
itorunit
torsunit
ptorunit
storunit
ttorunit
convertimproperdihedralenergytokcal/mole
convertimpropertorsionamplitudestokcal/mole
converttorsionalparameteramplitudestokcal/mole
convertpi-orbitaltorsionenergytokcal/mole
convertstretch-torsionenergytokcal/mole
convertstretch-torsionenergytokcal/mole
TORS
torsionalangleswithinthecurrentstructure
tors1
tors2
tors3
tors4
tors5
tors6
ntors
itors
1-foldamplitudeandphaseforeachtorsionalangle
2-foldamplitudeandphaseforeachtorsionalangle
3-foldamplitudeandphaseforeachtorsionalangle
4-foldamplitudeandphaseforeachtorsionalangle
5-foldamplitudeandphaseforeachtorsionalangle
6-foldamplitudeandphaseforeachtorsionalangle
totalnumberoftorsionalanglesinthesystem
numbersoftheatomsineachtorsionalangle
TORTOR
torsion-torsionsinthecurrentstructure
ntortor
itt
totalnumberoftorsion-torsioninteractions
atomsandparameterindicesfortorsion-torsion
TREE
potentialsmoothing&searchtreelevels
163
TINKERUser'sGuide
163
maxpss
etree
ilevel
nlevel
maximumnumberofpotentialsmoothinglevels
energyreferencevalueatthetopofthetree
smoothingdeformationvalueateachtreelevel
numberoflevelsofpotentialsmoothingused
UNITS
physicalconstantsandunitconversions
avogadro
boltzmann
gasconst
lightspd
bohr
joule
evolt
hartree
electric
debye
prescon
convert
Avogadro'snumber(N)inparticles/mole
Boltzmannconstant(kB)ing*Ang**2/ps**2/K/mole
idealgasconstant(R)inkcal/mole/K
speedoflightinvacuum(c)incm/ps
conversionfromBohrstoAngstroms
conversionfromcaloriestojoules
conversionfromHartreetoelectron-volts
conversionfromHartreetokcal/mole
conversionfromelectron**2/Angtokcal/mole
conversionfromelectron-AngtoDebyes
conversionfromkcal/mole/Ang**3toAtm
conversionfromkcaltog*Ang**2/ps**2
UREY
Urey-Bradleyinteractionsinthestructure
uk
ul
nurey
iury
Urey-Bradleyforceconstants(kcal/mole/Ang**2)
ideal1-3distancevaluesinAngstroms
totalnumberofUrey-Bradleytermsinthesystem
numbersoftheatomsineachUrey-Bradleyinteraction
URYPOT
specificsofUrey-Bradleyfunctionalform
cury
qury
ureyunit
cubiccoefficientinUrey-Bradleypotential
quarticcoefficientinUrey-Bradleypotential
convertUrey-Bradleyenergytokcal/mole
USAGE
atomsactiveduringenergycomputation
nuse
use
numberofactiveatomsusedinenergycalculation
trueifanatomisactive,falseifinactive
VDW
vanderWaalsparametersforcurrentstructure
radmin
epsilon
radmin4
epsilon4
radhbnd
epshbnd
kred
ired
nvdw
ivdw
minimumenergydistanceforeachatomclasspair
welldepthparameterforeachatomclasspair
minimumenergydistancefor1-4interactionpairs
welldepthparameterfor1-4interactionpairs
minimumenergydistanceforhydrogenbondingpairs
welldepthparameterforhydrogenbondingpairs
valueofreductionfactorparameterforeachatom
attachedatomfromwhichreductionfactorisapplied
totalnumbervanderWaalsactivesitesinthesystem
numberoftheatomforeachvanderWaalsactivesite
164
TINKERUser'sGuide
164
VDWPOT
specificsofvanderWaalsfunctionalform
abuck
bbuck
cbuck
ghal
dhal
v2scale
v3scale
v4scale
v5scale
igauss
ngauss
vdwtyp
radtyp
radsiz
radrule
epsrule
gausstyp
valueof"A"constantinBuckinghamvdwpotential
valueof"B"constantinBuckinghamvdwpotential
valueof"C"constantinBuckinghamvdwpotential
valueof"gamma"inbuffered14-7vdwpotential
valueof"delta"inbuffered14-7vdwpotential
factorbywhich1-2vdwinteractionsarescaled
factorbywhich1-3vdwinteractionsarescaled
factorbywhich1-4vdwinteractionsarescaled
factorbywhich1-5vdwinteractionsarescaled
coefficientsofGaussianfittovdwpotential
numberofGaussiansusedinfittovdwpotential
typeofvanderWaalspotentialenergyfunction
typeofparameter(sigmaorR-min)foratomicsize
atomicsizeprovidedasradiusordiameter
combiningruleforatomicsizeparameters
combiningruleforvdwwelldepthparameters
typeofGaussianfittovanderWaalspotential
VIRIAL
componentsofinternalvirialtensor
vir
totalinternalvirialCartesiantensorcomponents
WARP
parametersforpotentialsurfacesmoothing
m2
deform
difft
diffv
diffc
use_smooth
use_dem
use_gda
use_tophat
use_stophat
secondmomentoftheGDAgaussianforeachatom
valueofthesmoothingdeformationparameter
diffusioncoefficientfortorsionalpotential
diffusioncoefficientforvanderWaalspotential
diffusioncoefficientforcharge-chargepotential
flagtouseapotentialenergysmoothingmethod
flagtousediffusionequationmethodpotential
flagtousegaussiandensityannealingpotential
flagtouseanalyticaltophatsmoothedpotential
flagtouseshiftedtophatsmoothedpotential
XTALS
crystalstructuresforparameterfitting
e0_lattice
moment_0
nxtal
nvary
ivary
vary
iresid
rsdtyp
vartyp
ideallatticeenergyforthecurrentcrystal
idealdipolemomentformonomerfromcrystal
numberofcrystalstructurestobestored
numberofpotentialparameterstooptimize
indexforthetypesofpotentialparameters
atomnumbersinvolvedinpotentialparameters
crystalstructuretowhicheachresidualrefers
experimentalvariableforeachoftheresiduals
typeofpotentialparametertobeoptimized
ZCLOSE
ringopeningsandclosuresforZ-matrix
165
TINKERUser'sGuide
165
nadd
iadd
ndel
idel
numberofaddedbondsbetweenZ-matrixatoms
numbersoftheatompairsdefiningaddedbonds
numberofbondsbetweenZ-matrixbondstodelete
numbersoftheatompairsdefiningdeletedbonds
ZCOORD
Z-matrixinternalcoordinatedefinitions
zbond
zang
ztors
iz
bondlengthusedtodefineeachZ-matrixatom
bondangleusedtodefineeachZ-matrixatom
angleortorsionusedtodefineZ-matrixatom
definingatomnumbersforeachZ-matrixatom
166
TINKERUser'sGuide
166
11.
IndexofFunction&SubroutineCalls
This section contains an alphabetical cross index listing of the routines called by each TINKER
program, subroutine and function. Routines not present in this list do not make calls to any other
portionoftheTINKERpackage.
Routine
ListofSourceCodeUnitscalledbythisRoutine
ACTIVE
GETTEXT
UPCASE
ADDBASE
ADDBOND
FINDATM
OVERLAP
JACOBI
PIALTER
NEWATM
PIMOVE
OLDATM
PITILT
ADDSIDE
ADDBASE
ADDBOND
JACOBI
PIALTER
VERSION
FATAL
NEWATM
PIMOVE
FINDATM
OLDATM
PITILT
FREEUNIT
OVERLAP
PRTSEQ
ALCHEMY
ENERGY
FINAL
HATOM
NUMERAL
FREEUNIT
HYBRID
READXYZ
GETTEXT
INITIAL
UPCASE
GETXYZ
MECHANIC
VERSION
ANALYSIS
BOUNDS
EANGANG3
ECHARGE3
EGEOM3
ELJ3
EOPBEND3
ESOLV3
ETORTOR3
REPLICA
EANGLE3
ECHGDPL3
EHAL3
EMETAL3
EOPDIST3
ESTRBND3
EUREY3
EBOND3
EDIPOLE3
EIMPROP3
EMM3HB3
EPITORS3
ESTRTOR3
EXTRA3
EBUCK3
EGAUSS3
EIMPTOR3
EMPOLE3
ERXNFLD3
ETORS3
PISCF
ANALYZE
ANALYZ4
ANALYZ6
FINAL
MECHANIC
READXYZ
VERSION
ANALYZ8
FREEUNIT
NEXTARG
SUFFIX
ATOMYZE
GETXYZ
PARAMYZE
TRIMTEXT
ENRGYZE
INITIAL
PROPYZE
UPCASE
ANGLES
FATAL
ANNEAL
BEEMAN
FINAL
MDINIT
RGDSTEP
UPCASE
GETTEXT
MDREST
SDSTEP
VERLET
GETXYZ
MECHANIC
SHAKEUP
INITIAL
NEXTARG
SIGMOID
ARCHIVE
ACTIVE
BASEFILE
INITIAL
PRTCAR
SUFFIX
FINAL
NEXTARG
PRTXMOL
TRIMTEXT
FREEUNIT
NUMERAL
PRTXYZ
UPCASE
GETTEXT
PRTARC
READXYZ
VERSION
167
TINKERUser'sGuide
167
ATTACH
FATAL
SORT
BASEFILE
CONTROL
GETKEY
TRIMTEXT
BCUINT
BCUCOF
BCUINT1
BCUCOF
BCUINT2
BCUCOF
BEEMAN
GRADIENT
KINETIC
RATTLE
MDSAVE
RATTLE2
BETAI
BETACF
GAMMLN
BIGBLOCK
CELLATOM
BITORS
FATAL
BONDS
FATAL
BORN
SURFATOM
BSET
BMAX
BSSTEP
FATAL
CALENDAR
DATE_AND_TIME
CERROR
FATAL
CFFTB
CFFTB1
CFFTB1
PASSB
CFFTF
CFFTF1
CFFTF1
PASSF
CFFTI
CFFTI1
CHKTREE
LOCALXYZ
CIRPLN
MMID
MDSTAT
TEMPER
PRESSURE
TEMPER2
PZEXTR
TRIMTEXT
PASSB2
PASSB3
PASSB4
PASSB5
PASSF2
PASSF3
PASSF4
PASSF5
ANORM
DOT
VCROSS
VNORM
CLIMBER
ENERGY
GETREF
LOCALMIN
MAKEINT
CLIMBRGD
ENERGY
LOCALRGD
RIGIDXYZ
168
TINKERUser'sGuide
MAKEXYZ
168
CLIMBROT
ENERGY
LOCALROT
MAKEXYZ
CLIMBTOR
CHKTREE
ENERGY
MAKEXYZ
GETREF
LOCALXYZ
CLIMBXYZ
CHKTREE
ENERGY
GETREF
LOCALXYZ
CLUSTER
CUTOFFS
FATAL
UPCASE
GETNUMB
GETTEXT
SORT SORT3
COMMAND
GETARG
UPCASE
COMPRESS
CERROR
GETTOR
CONNECT
SORT
CONNOLLY
COMPRESS
CONTACT
TORUS
NEIGHBOR
VAM
PLACE
SADDLES
CONTACT
ANORM
CERROR
PTINCY
CONTROL
GETTEXT
UPCASE
COORDS
GYRATE
RMSERROR
CORRELATE
FINAL
INITIAL
TRIMTEXT
NEXTARG
PROPERTY
READBLK
CRYSTAL
BIGBLOCK
BOUNDS
GETTEXT
LATTICE
SYMMETRY
FIELD
GETXYZ
MOLECULE
UNITCELL
FINAL
INITIAL
NEXTARG
UPCASE
FREEUNIT
KATOM
PRTXYZ
VERSION
CUTOFFS
GETTEXT
UPCASE
CYTSY
CYTSYP
CYTSYS
DEPTH
DOT
VCROSS
DIAGQ
GETIME
SETIME
DIFFEQ
BSSTEP
GDASTAT
GVALUE
DIFFUSE
BASEFILE
FATAL
INITIAL
READXYZ
FIELD
KATOM
SUFFIX
FINAL
MOLECULE
UNITCELL
FREEUNIT
NEXTARG
VERSION
DISTGEOM
ACTIVE
ANGLES
FATAL
GETIME
ATTACH
FINAL
GETTEXT
BONDS
FREEUNIT
GETXYZ
EMBED
GEODESIC
GRAFIC
169
MAKEINT
VNORM
TINKERUser'sGuide
169
IMPOSE
MAKEREF
SETIME
VERSION
INITIAL
NEXTARG
TORSIONS
KCHIRAL
NUMERAL
TRIFIX
KGEOM
PRTXYZ
UPCASE
DMDUMP
GRAFIC
DOCUMENT
FINAL
FREEUNIT
INITIAL
PRTPRM
SUFFIX
GETPRM
LOWCASE
SORT10
TRIMTEXT
GETTEXT
NEXTARG
SORT6
UPCASE
GETWORD
NEXTTEXT
SORT7
VERSION
DSTMAT
GETIME
GETNUMB
SETIME
GETTEXT
SORT2
INVBETA
TRIFIX
RANDOM
UPCASE
DYNAMIC
BEEMAN
FINAL
MDREST
SDSTEP
GETXYZ
MECHANIC
SHAKEUP
INITIAL
NEXTARG
VERLET
MDINIT
RGDSTEP
EANGANG
GROUPS
IMAGE
EANGANG1
GROUPS
IMAGE
EANGANG2
EANGANG2A
GROUPS
EANGANG2A
IMAGE
EANGANG3
GROUPS
IMAGE
EANGLE
GROUPS
IMAGE
EANGLE1
GROUPS
IMAGE
EANGLE2
EANGLE2A
EANGLE2B
EANGLE2A
GROUPS
IMAGE
EANGLE2B
IMAGE
EANGLE3
GROUPS
IMAGE
EBOND
GROUPS
IMAGE
EBOND1
GROUPS
IMAGE
EBOND2
GROUPS
IMAGE
EBOND3
GROUPS
IMAGE
EBUCK
EBUCK0A
EBUCK0B
170
GROUPS
EBUCK0C
TINKERUser'sGuide
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170
EBUCK0A
GROUPS
IMAGE
SWITCH
EBUCK0B
GROUPS
LIGHTS
SWITCH
EBUCK0C
EGAUSS
EBUCK1
EBUCK1A
EBUCK1B
EBUCK1C
EBUCK1A
GROUPS
IMAGE
SWITCH
EBUCK1B
GROUPS
LIGHTS
SWITCH
EBUCK1C
EGAUSS1
EBUCK2
EBUCK2A
EBUCK2B
FATAL
EBUCK2A
GROUPS
IMAGE
SWITCH
EBUCK2B
EGAUSS2
EBUCK3
EBUCK3A
EBUCK3B
EBUCK3C
EBUCK3A
GROUPS
IMAGE
SWITCH
EBUCK3B
GROUPS
LIGHTS
SWITCH
EBUCK3C
EGAUSS3
ECHARGE
ECHARGE0A
ECHARGE0B
ECHARGE0C
ECHARGE0A
GROUPS
IMAGE
SWITCH
ECHARGE0B
GROUPS
LIGHTS
SWITCH
ECHARGE0C
ERF
GROUPS
ECHARGE0D
EPME
ERFC
ECHARGE0E
EPME
ECHARGE1
FATAL
FATAL
ECHARGE0D
ECHARGE0E
GROUPS
IMAGE
SWITCH
ERFC
GROUPS
LIGHTS
SWITCH
ECHARGE1A
ECHARGE1B
ECHARGE1C
ECHARGE1D
ECHARGE1A
GROUPS
IMAGE
SWITCH
ECHARGE1B
GROUPS
LIGHTS
SWITCH
ECHARGE1C
ERF
GROUPS
171
TINKERUser'sGuide
171
ECHARGE1D
EPME1
ERFC
GROUPS
IMAGE
SWITCH
ECHARGE2
ECHARGE2A
ECHARGE2B
ECHARGE2C
ECHARGE2A
GROUPS
IMAGE
SWITCH
ECHARGE2B
ERF
GROUPS
ECHARGE2C
ERFC
GROUPS
IMAGE
ECHARGE3
ECHARGE3A
ECHARGE3B
ECHARGE3C
ECHARGE3D
ECHARGE3E
ECHARGE3A
GROUPS
IMAGE
SWITCH
ECHARGE3B
GROUPS
LIGHTS
SWITCH
ECHARGE3C
ERF
GROUPS
ECHARGE3D
EPME3
ERFC
GROUPS
IMAGE
SWITCH
ECHARGE3E
EPME3
ERFC
GROUPS
LIGHTS
SWITCH
ECHGDPL
GROUPS
IMAGE
SWITCH
ECHGDPL1
GROUPS
IMAGE
SWITCH
ECHGDPL2
GROUPS
IMAGE
SWITCH
ECHGDPL3
GROUPS
IMAGE
SWITCH
EDIPOLE
GROUPS
IMAGE
SWITCH
EDIPOLE1
GROUPS
IMAGE
SWITCH
EDIPOLE2
GROUPS
IMAGE
SWITCH
EDIPOLE3
GROUPS
IMAGE
SWITCH
EGAUSS
EGAUSS0A
EGAUSS0B
EGAUSS0A
GROUPS
SWITCH
EGAUSS0B
ERF
GROUPS
EGAUSS1
EGAUSS1A
EGAUSS1B
EGAUSS1A
GROUPS
SWITCH
EGAUSS1B
ERF
GROUPS
172
TINKERUser'sGuide
172
EGAUSS2
EGAUSS2A
EGAUSS2B
EGAUSS2A
GROUPS
SWITCH
EGAUSS2B
GROUPS
EGAUSS3
EGAUSS3A
EGAUSS3B
EGAUSS3A
GROUPS
SWITCH
EGAUSS3B
ERF
GROUPS
EGBSA0A
GROUPS
SWITCH
EGBSA0B
ERF
GROUPS
EGBSA1A
GROUPS
SWITCH
EGBSA1B
ERF
GROUPS
EGBSA2A
SWITCH
EGBSA2B
ERF
EGBSA3A
GROUPS
SWITCH
EGBSA3B
ERF
GROUPS
EGEOM
GROUPS
IMAGE
EGEOM1
GROUPS
IMAGE
EGEOM2
GROUPS
IMAGE
EGEOM3
GROUPS
IMAGE
EHAL
EHAL0A
EHAL0B
EHAL0A
GROUPS
IMAGE
SWITCH
EHAL0B
GROUPS
LIGHTS
SWITCH
EHAL1
EHAL1A
EHAL1B
EHAL1A
GROUPS
IMAGE
SWITCH
EHAL1B
GROUPS
LIGHTS
SWITCH
173
TINKERUser'sGuide
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EHAL2
GROUPS
IMAGE
EHAL3
EHAL3A
EHAL3B
EHAL3A
GROUPS
IMAGE
SWITCH
EHAL3B
GROUPS
LIGHTS
SWITCH
EIGEN
GETIME
POWER
SETIME
EIGENRGD
DIAGQ
HESSRGD
EIGENROT
DIAGQ
HESSROT
EIGENROT
DIAGQ
HESSROT
EIGENTOR
DIAGQ
HESSROT
EIGENXYZ
DIAGQ
HESSIAN
EIMPROP
GROUPS
IMAGE
EIMPROP1
GROUPS
IMAGE
EIMPROP2
GROUPS
IMAGE
EIMPROP3
GROUPS
IMAGE
EIMPTOR
GROUPS
IMAGE
EIMPTOR1
GROUPS
IMAGE
EIMPTOR2
GROUPS
IMAGE
EIMPTOR3
GROUPS
IMAGE
ELJ
ELJ0A
ELJ0B
ELJ0C
ELJ0A
GROUPS
IMAGE
SWITCH
ELJ0B
GROUPS
LIGHTS
SWITCH
ELJ0C
EGAUSS
ELJ0D
GROUPS
ELJ1
ELJ1A
ELJ1B
ELJ1C
ELJ1A
GROUPS
IMAGE
SWITCH
174
SWITCH
TINKERUser'sGuide
ELJ0D
ELJ1D
174
ELJ1B
GROUPS
ELJ1C
EGAUSS1
ELJ1D
GROUPS
ELJ2
ELJ2A
ELJ2B
ELJ2A
GROUPS
IMAGE
SWITCH
ELJ2B
EGAUSS2
ELJ2C
GROUPS
ELJ3
ELJ3A
ELJ3B
ELJ3C
ELJ3A
GROUPS
IMAGE
SWITCH
ELJ3B
GROUPS
LIGHTS
SWITCH
ELJ3C
EGAUSS3
ELJ3D
GROUPS
EMBED
BNDERR
CHIRER
DSTMAT
FREEUNIT
LOCERR
PRTXYZ
TORSER
CHKSIZE
EIGEN
GETIME
MAJORIZE
REFINE
VDWERR
EMETAL
FATAL
EMETAL1
FATAL
EMETAL3
EMETAL
EMM3HB
EMM3HB0A
EMM3HB0B
EMM3HB0A
GROUPS
IMAGE
SWITCH
EMM3HB0B
GROUPS
LIGHTS
SWITCH
EMM3HB1
EMM3HB1A
EMM3HB1B
EMM3HB1A
GROUPS
IMAGE
SWITCH
EMM3HB1B
GROUPS
LIGHTS
SWITCH
175
LIGHTS
SWITCH
TINKERUser'sGuide
ELJ3D
COORDS
EXPLORE
GYRATE
METRIC
RMSERROR
DMDUMP
FRACDIST
IMPOSE
NUMERAL
SETIME
175
EMM3HB2
GROUPS
IMAGE
EMM3HB3
EMM3HB3A
EMM3HB3B
EMM3HB3A
GROUPS
IMAGE
SWITCH
EMM3HB3B
GROUPS
LIGHTS
SWITCH
EMPOLE
EMPOLE0A
EMPOLE0B
EMPOLE0A
CHKPOLE
GROUPS
SWITCH
IMAGE
INDUCE
ROTPOLE
EMPOLE0B
CHKPOLE
EREAL
ERECIP
INDUCE
ROTPOLE
EMPOLE1
EMPOLE1A
EMPOLE1B
EMPOLE1A
CHKPOLE
GROUPS
SWITCH
IMAGE
TORQUE
INDUCE
TORQUE1
ROTPOLE
EMPOLE1B
CHKPOLE
EREAL1
TORQUE
ERECIP1
INDUCE
ROTPOLE
EMPOLE2
EMPOLE2A
EMPOLE2A
GROUPS
IMAGE
SWITCH
TORQUE
EMPOLE3
EMPOLE3A
EMPOLE3B
EMPOLE3A
CHKPOLE
GROUPS
SWITCH
IMAGE
INDUCE
ROTPOLE
EMPOLE3B
CHKPOLE
EREAL3
ERECIP3
INDUCE
ROTPOLE
ENERGY
BOUNDS
EANGANG
ECHARGE
EGEOM
ELJ
EOPBEND
ESOLV
ETORTOR
REPLICA
EANGLE
ECHGDPL
EHAL
EMETAL
EOPDIST
ESTRBND
EUREY
EBOND
EDIPOLE
EIMPROP
EMM3HB
EPITORS
ESTRTOR
EXTRA
EBUCK
EGAUSS
EIMPTOR
EMPOLE
ERXNFLD
ETORS
PISCF
ENRGYZE
ANALYSIS
EOPBEND
GROUPS
IMAGE
EOPBEND1
GROUPS
IMAGE
176
SWITCH
TINKERUser'sGuide
176
EOPBEND2
EOPBEND2A
EOPBEND2A
IMAGE
EOPBEND3
GROUPS
IMAGE
EOPDIST
GROUPS
IMAGE
EOPDIST1
GROUPS
IMAGE
EOPDIST2
GROUPS
IMAGE
EOPDIST3
GROUPS
IMAGE
EPITORS
GROUPS
IMAGE
EPITORS1
GROUPS
IMAGE
EPITORS2
EPITORS2A
GROUPS
EPITORS2A
IMAGE
EPITORS3
GROUPS
IMAGE
EPME
BSPLINE
FFTFRONT
EPME1
BSPLINE1
FFTBACK
EPME3
BSPLINE
FFTFRONT
EPUCLC
ANORM
EREAL
ERFC
IMAGE
SWITCH
EREAL1
ERFC
IMAGE
SWITCH
EREAL3
ERFC
IMAGE
SWITCH
ERECIP1
TORQUE
ERF
ERFCORE
ERFC
ERFCORE
ERFIK
D1D2
RFINDEX
ERFINV
ERF
FATAL
ERXNFLD
CHKPOLE
ERFIK
177
GROUPS
FFTFRONT
IJKPTS
TINKERUser'sGuide
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TORQUE1
ROTPOLE
SWITCH
177
ERXNFLD3
CHKPOLE
ERFIK
IJKPTS
ROTPOLE
ESOLV
BORN
EGBSA0A
EGBSA0B
SURFACE
ESOLV1
BORN
BORN1
EGBSA1A
EGBSA1B
ESOLV2
EGBSA2A
EGBSA2B
ESOLV3
BORN
EGBSA3A
EGBSA3B
SURFACE
ESTRBND
GROUPS
IMAGE
ESTRBND1
GROUPS
IMAGE
ESTRBND2
GROUPS
IMAGE
ESTRBND3
GROUPS
IMAGE
ESTRTOR
GROUPS
IMAGE
ESTRTOR1
GROUPS
IMAGE
ESTRTOR2
GROUPS
IMAGE
ESTRTOR3
GROUPS
IMAGE
ETORS
ETORS0A
ETORS0B
ETORS0A
GROUPS
IMAGE
ETORS0B
GROUPS
ETORS1
ETORS1A
ETORS1B
ETORS1A
GROUPS
IMAGE
ETORS1B
GROUPS
ETORS2
ETORS2A
ETORS2B
ETORS2A
GROUPS
IMAGE
ETORS2B
GROUPS
ETORS3
ETORS3A
ETORS3B
ETORS3A
GROUPS
IMAGE
178
TINKERUser'sGuide
SWITCH
SURFACE
178
ETORS3B
GROUPS
ETORTOR
BCUINT
GROUPS
IMAGE
ETORTOR1
BCUINT1
GROUPS
IMAGE
ETORTOR2
BCUINT2
GROUPS
IMAGE
ETORTOR3
BCUINT
GROUPS
IMAGE
EUREY
GROUPS
IMAGE
EUREY1
GROUPS
IMAGE
EUREY2
GROUPS
IMAGE
EUREY3
GROUPS
IMAGE
EWALDCOF
ERFC
EXPLORE
INITERR
FFTBACK
CFFTB
FFTFRONT
CFFTF
FFTSETUP
CFFTI
FIELD
GETPRM
FINAL
SKTKILL
FRACDIST
DIST2
FREEUNIT
FATAL
GDA
DIFFEQ
FINAL
GETXYZ
NUMERAL
VERSION
GDA1
GRADIENT
HESSIAN
GDA2
GRADIENT
GDA3
HESSIAN
GDASTAT
ENERGY
179
MIDERR
SIGMOID
TOTERR
FREEUNIT
INITIAL
PRTXYZ
GDASTAT
MECHANIC
RANDOM
PRMKEY
TRIMTEXT
GYRATE
GETTEXT
NEXTARG
TNCGUPCASE
OPTSAVE
TINKERUser'sGuide
179
GEODESIC
MINPATH
GETBASE
PDBATM
GETIME
CLOCK
GETINT
BASEFILE
CHKXYZ
MAKEXYZ
VERSION
CONNECT
NEXTARG
FATAL
READINT
FREEUNIT
SUFFIX
GETKEY
FATAL
FREEUNIT
UPCASE
GETTEXT
SUFFIX
TRIMTEXT
GETMOL2
BASEFILE
FREEUNIT
VERSION
NEXTARG
READMOL2
SUFFIX
GETNUCH
PDBATM
GETNUMB
TRIMTEXT
GETPDB
BASEFILE
FREEUNIT
VERSION
NEXTARG
READPDB
SUFFIX
GETPRB
DIST2
DOT
GETTOR
VCROSS
GETPRM
FATAL
FREEUNIT
READPRM
VERSION
GETTEXT
SUFFIX
INITPRM
TRIMTEXT
GETPROH
PDBATM
GETSEQ
GETWORD
TRIMTEXT
UPCASE
GETSEQN
GETTEXT
GETWORD
TRIMTEXT
UPCASE
GETSIDE
PDBATM
GETTOR
DIST2
GETXYZ
BASEFILE
FATAL
SUFFIX
FREEUNIT
VERSION
NEXTARG
READXYZ
GRADIENT
BOUNDS
EANGANG1
ECHARGE1
EGEOM1
ELJ1
EOPBEND1
ESOLV1
ETORTOR1
REPLICA
EANGLE1
ECHGDPL1
EHAL1
EMETAL1
EOPDIST1
ESTRBND1
EUREY1
EBOND1
EDIPOLE1
EIMPROP1
EMM3HB1
EPITORS1
ESTRTOR1
EXTRA1
EBUCK1
EGAUSS1
EIMPTOR1
EMPOLE1
ERXNFLD1
ETORS1
PISCF
180
SORT3
TINKERUser'sGuide
NEXTARG
UPCASE
180
GRADRGD
GRADIENT
GRADROT
GRADIENT
HANGLE
NUMERAL
HBOND
NUMERAL
HDIPOLE
NUMERAL
HESSIAN
BORN
BOUNDS
EBOND2
EDIPOLE2
EIMPROP2
EMM3HB2
EPITORS2
ESTRTOR2
EXTRA2
REPLICA
HESSRGD
GRADRGD
RIGIDXYZ
HESSROT
GRADROT
MAKEXYZ
HIMPTOR
NUMERAL
HSTRTOR
NUMERAL
HTORS
NUMERAL
HYBRID
HANGLE
IMPOSE
ROTLIST
CHKPOLE
EBUCK2
EGAUSS2
EIMPTOR2
EMPOLE2
ERXNFLD2
ETORS2
FATAL
ROTPOLE
EANGANG2
ECHARGE2
EGEOM2
ELJ2
EOPBEND2
ESOLV2
ETORTOR2
INDUCE
EANGLE2
ECHGDPL2
EHAL2
EMETAL2
EOPDIST2
ESTRBND2
EUREY2
PISCF
HATOM
HIMPTOR
HVDW
HBOND
HSTRBND
HCHARGE
HSTRTOR
HDIPOLE
HTORS
CENTER
QUATFIT
RMSFIT
INDUCE
INDUCE0A
INDUCE0B
INDUCE0A
FATAL
GROUPS
IMAGE
PRTERR
SWITCH
INDUCE0B
FATAL
PRTERR
UMUTUAL2
UDIRECT1
UDIRECT2
UMUTUAL1
INEDGE
CERROR
INERTIA
JACOBI
INITERR
LOCERR
181
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181
INITIAL
COMMAND
INITRES
PRECISE
PROMO
INITROT
FATAL
NEXTARG
ROTCHECK
ROTLIST
INTEDIT
FIELD
FINAL
GETWORD
PRTINT
ZHELP
FREEUNIT
INITIAL
TRIMTEXT
ZVALUE
GEOMETRY
MAKEXYZ
UPCASE
GETINT
NUMBER
VERSION
INTXYZ
FINAL
FREEUNIT
VERSION
GETINT
INITIAL
PRTXYZ
INVBETA
BETAI
GAMMLN
INVERT
FATAL
IPEDGE
CERROR
ISPLPE
CYTSY
CYTSYS
KANGANG
GETTEXT
UPCASE
KANGLE
GETTEXT
NUMERAL
UPCASE
KATOM
GETNUMB
GETSTRING
GETTEXT
UPCASE
KBOND
GETTEXT
KENEG
NUMERAL
UPCASE
KCHARGE
GETTEXT
UPCASE
KDIPOLE
GETTEXT
NUMERAL
UPCASE
KENEG
GETTEXT
NUMERAL
UPCASE
KEWALD
EWALDCOF
FATAL
UPCASE
FFTSETUP
GETTEXT
MODULI
KGEOM
FATAL
GEOMETRY
UPCASE
GETTEXT
GETWORD
IMAGE
KIMPROP
GETTEXT
NUMERAL
UPCASE
KIMPTOR
GETTEXT
NUMERAL
TORPHASE
UPCASE
KMPOLE
CHKPOLE
GETTEXT
SORT3
NUMBER
UPCASE
NUMERAL
KOPBEND
GETTEXT
NUMBER
NUMERAL
UPCASE
182
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182
KOPDIST
GETTEXT
NUMERAL
UPCASE
KORBIT
GETTEXT
NUMERAL
UPCASE
KPITORS
GETTEXT
NUMERAL
UPCASE
KPOLAR
CHKPOLE
GETTEXT
POLARGRP
UPCASE
KSOLV
GETTEXT
GETWORD
KANGLE
KBOND
KSTRBND
GETTEXT
UPCASE
KSTRTOR
GETTEXT
NUMERAL
UPCASE
KTORS
GETTEXT
NUMERAL
TORPHASE
UPCASE
KTORTOR
GETTEXT
ISPLPE
NUMERAL
SORT9
KUREY
GETTEXT
NUMERAL
UPCASE
KVDW
GETTEXT
NUMBER
NUMERAL
UPCASE
LBFGS
COMMENT'
GETTEXT
OPTSAVE
SEARCH
LIGASE
FINDATM
LIGHTS
FATAL
SORT2
SORT5
LMSTEP
PRECISE
QRSOLVE
LOCALMIN
GRADIENT
TNCG
LOCALRGD
OCVM
LOCALROT
OCVM
LOCALXYZ
TNCG
MAJORIZE
GETIME
GYRATE
RMSERROR
SETIME
MAKEINT
ADJACENT
FATAL
GEOMETRY
GETTEXT
UPCASE
MAKEPDB
ATTACH
FREEUNIT
GETSIDE
VERSION
GETBASE
NUMERAL
GETNUCH
PDBATM
GETPROH
READSEQ
MAKEXYZ
XYZATM
MAPCHECK
FREEUNIT
NUMERAL
PRTXYZ
VERSION
183
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UPCASE
UPCASE
UPCASE
183
MAXWELL
ERFINV
MCM1
GRADIENT
MCM2
HESSIAN
MCMSTEP
TNCG
MDINIT
FREEUNIT
MDREST
INVERT
MDSAVE
RANDOM
GETTEXT
LATTICE
RANVEC
GETWORD
MAXWELL
READDYN
GRADIENT
MDREST
UPCASE
GRPLINE
NUMERAL
VERSION
FATAL
FREEUNIT
PRTXYZ
VERSION
NUMERAL
SKTDYN
OPENEND
SUFFIX
PRTDYN
TRIMTEXT
MEASFN
CERROR
TRIPLE
VCROSS
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MEASFP
CERROR
DOT
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MEASFS
CERROR
DOT
VECANG
VNORM
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MECHANIC
ACTIVE
ANGLES
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KANGANG
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KOPBEND
KPOLAR
KTORS
LATTICE
POLYMER
UNITCELL
ATTACH
CUTOFFS
KANGLE
KDIPOLE
KIMPTOR
KOPDIST
KSOLV
KTORTOR
MOLECULE
RINGS
BITORS
FATAL
KATOM
KEWALD
KMETAL
KORBIT
KSTRBND
KUREY
MUTATE
SMOOTH
MERGE
FATAL
GETREF
MIDERR
BNDERR
CHIRER
LOCERR
TORSER
MINIMIZ1
GRADIENT
MINIMIZE
FINAL
FREEUNIT
INITIAL
PRTXYZ
GETTEXT
LBFGS
UPCASE
GETXYZ
MECHANIC
VERSION
184
TINKERUser'sGuide
BONDS
FIELD
KBOND
KGEOM
KMPOLE
KPITORS
KSTRTOR
KVDW
ORBITAL
TORSIONS
GRADIENT
NEXTARG
184
MINIROT
FINAL
FREEUNIT
INITIAL
NEXTARG
GETINT
INITROT
PRTINT
GETTEXT
LBFGS
UPCASE
GRADROT
MECHANIC
VERSION
MINIROT1
GRADROT
MAKEXYZ
MINRIGID
FINAL
FREEUNIT
INITIAL
ORIENT
GETTEXT
LBFGS
PRTXYZ
GETXYZ
MECHANIC
UPCASE
GRADRGD
NEXTARG
VERSION
MINRIGID1
GRADRGD
RIGIDXYZ
MMID
GVALUE
MODECART
CLIMBXYZ
EIGENXYZ
GETREF
IMPOSE
MAKEREF
MODEROT
CLIMBROT
EIGENROT
MAKEXYZ
MODESRCH
CLIMBER
EIGENROT
MAKEINT
MAKEREF
MAPCHECK
MODETORS
CLIMBTOR
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MAKEREF
GETREF
IMPOSE
MAKEINT
MODULI
BSPLINE
DFTMOD
MOLECULE
SORT
SORT3
MOLUIND
UFIELD
MOMENTS
CHKPOLE
INDUCE
JACOBI
ROTPOLE
MONTE
CHKCLASH
FREEUNIT
INITIAL
MAKEXYZ
PRTXYZ
VERSION
GETREF
INITROT
MCMSTEP
RANDOM
GETTEXT
MAKEINT
MECHANIC
RANVEC
GETXYZ
MAKEREF
NEXTARG
UPCASE
MUTATE
GETTEXT
UPCASE
NEIGHBOR
CERROR
DIST2
NEWATM
ADDBOND
XYZATM
NEWTON
FINAL
FREEUNIT
INITIAL
TNCG
GETTEXT
MECHANIC
UPCASE
GETXYZ
NEXTARG
VERSION
GRADIENT
PRTXYZ
NEWTON1
GRADIENT
NEWTON2
HESSIAN
185
TINKERUser'sGuide
185
NEWTROT
FINAL
FREEUNIT
INITIAL
PRTINT
GETINT
INITROT
TNCG
GETTEXT
MECHANIC
UPCASE
NEWTROT1
GRADROT
MAKEXYZ
NEWTROT2
HESSROT
MAKEXYZ
NORMAL
RANDOM
NUCBASE
OCVM
NUCCHAIN
ORIENT
POTOFF
ZATOM
NUCBASE
OCVM
ORIENT
ZATOM
NUCLEIC
BASEFILE
CONNECT
GETKEY
MAKEXYZ
PRTINT
VERSION
DELETE
GETSEQN
MOLECULE
PRTSEQ
WATSON
FIELD
INITIAL
NEXTARG
PRTXYZ
NUMBER
TRIMTEXT
OCVM
GETTEXT
OPTSAVE
PRECISE
UPCASE
OLDATM
ADDBOND
FATAL
OPTIMIZ1
GRADIENT
OPTIMIZE
FATAL
FINAL
GRADIENT
OCVM
FREEUNIT
INITIAL
PRTXYZ
GETTEXT
MECHANIC
UPCASE
GETXYZ
NEXTARG
VERSION
OPTIROT
FATAL
FINAL
GRADROT
NEXTARG
VERSION
FREEUNIT
INITIAL
OCVM
GETINT
INITROT
PRTINT
GETTEXT
MECHANIC
UPCASE
OPTIROT1
GRADROT
MAKEXYZ
OPTRIGID
FATAL
FINAL
GRADRGD
OCVM
VERSION
FREEUNIT
INITIAL
ORIENT
GETTEXT
MECHANIC
PRTXYZ
GETXYZ
NEXTARG
UPCASE
OPTRIGID1
GRADRGD
RIGIDXYZ
OPTSAVE
FATAL
FREEUNIT
PRTINT
VERSION
MAKEXYZ
PRTXYZ
NUMERAL
SKTOPT
OPENEND
SUFFIX
186
TINKERUser'sGuide
GRADROT
NEXTARG
VERSION
FREEUNIT
MAKEINT
NUCCHAIN
TRIMTEXT
186
ORBITAL
FATAL
GETTEXT
PIPLANE
UPCASE
ORIENT
XYZRIGID
OVERLAP
SLATER
PATH
FINAL
GETXYZ
LBFGS
ORTHOG
IMPOSE
MECHANIC
POTNRG
INITIAL
NEXTARG
INVERT
OPTSAVE
PATH1
POTNRG
PATHPNT
OCVM
PATHSCAN
PATHPNT
SADDLE1
TANGENT
PATHVAL
IMPOSE
PDBXYZ
CHKXYZ
DELETE
GETNUMB
PRTXYZ
VERSION
FIELD
GETPDB
RIBOSOME
FINAL
INITIAL
SORT
FREEUNIT
LIGASE
UPCASE
PIPLANE
FATAL
PISCF
NEWATM
PITILT
OLDATM
PLACE
CERROR
DIST2
GETPRB
GETTOR
INEDGE
POLARGRP
SORT
SORT8
POLARIZE
FATAL
GETXYZ
MOLUIND
INITIAL
JACOBI
MECHANIC
POLYMER
FATAL
GETTEXT
IMAGE
UPCASE
POTNRG
GRADIENT
POWER
RANDOM
PRECOND
CHOLESKY
PRESSURE
LATTICE
PRMKEY
GETTEXT
POTOFF
UPCASE
187
COLUMN
GETWORD
TINKERUser'sGuide
187
PROCHAIN
GETTEXT
PROSIDE
UPCASE
ZATOM
PROJCT
DOT
PROPYZE
GRADIENT
GYRATE
INERTIA
MOMENTS
PROSIDE
FREEUNIT
PRTINT
PRTXYZ
VERSION
ZATOM
PROTEIN
BASEFILE
CHKXYZ
FREEUNIT
MAKEINT
PRTINT
VERSION
CONNECT
GETKEY
MAKEXYZ
PRTSEQ
DELETE
GETSEQ
NEXTARG
PRTXYZ
FIELDFINAL
INITIAL
PROCHAIN
TRIMTEXT
PRTARC
VERSION
PRTCAR
VERSION
PRTDYN
ZATOM
PRTERR
ZATOM
PRTINT
VERSION
PRTMOL2
NUMBER
PRTPDB
VERSION
PRTPRM
NUMBER
PRTSEQ
VERSION
PRTXMOL
VERSION
PRTXYZ
VERSION
PSS
ACTIVE
GETTEXT
INITROT
MECHANIC
PSSWRITE
GETXYZ
LOCALXYZ
MODECART
SIGMOID
IMPOSE
MAKEINT
MODETORS
UPCASE
PSS1
GRADIENT
PSS2
HESSIAN
PSSRGD1
GRADRGD
RIGIDXYZ
PSSRIGID
FINAL
FREEUNIT
INITIAL
NUMERAL
GETTEXT
MAKEREF
OCVM
GETXYZ
MECHANIC
ORIENT
IMPOSE
NEXTARG
PRTXYZ
188
VERSION
FINAL
INITIAL
MAKEREF
NEXTARG
TINKERUser'sGuide
188
RGDSRCH
VERSION
RIGIDXYZ
SIGMOID
UPCASE
PSSROT
FINAL
FREEUNIT
INITIAL
MECHANIC
OCVM
GETTEXT
INITROT
MODEROT
PRTXYZ
GETXYZ
MAKEREF
NEXTARG
UPCASE
IMPOSE
MAKEXYZ
NUMERAL
VERSION
PSSROT1
GRADROT
MAKEXYZ
PSSWRITE
FREEUNIT
NUMERAL
PRTXYZ
VERSION
PTINCY
DOT
EPUCLC
PROJCT
ROTANG
QUATFIT
JACOBI
RADIAL
BASEFILE
FATAL
GETWORD
MOLECULE
UNITCELL
FINAL
IMAGE
NEXTARG
UPCASE
FREEUNIT
INITIAL
READXYZ
VERSION
RANDOM
CALENDAR
GETTEXT
UPCASE
RANVEC
RANDOM
RATTLE
FATAL
IMAGE
PRTERR
RATTLE2
FATAL
IMAGE
PRTERR
READBLK
FATAL
FREEUNIT
GETWORD
NUMERAL
READDYN
FATAL
VERSION
READINT
FATAL
GETTEXT
VERSION
GETWORD
NEXTTEXT
TRIMTEXT
READMOL2
FATAL
GETTEXT
UPCASE
GETWORD
VERSION
SORT
TRIMTEXT
READPDB
FATAL
FIXPDB
UPCASE
GETTEXT
VERSION
NEXTARG
TRIMTEXT
READPRM
FATAL
GETNUMB
NUMERAL
TRIMTEXT
GETSTRING
PRMKEY
UPCASE
GETTEXT
SORT9
GETWORD
TORPHASE
READSEQ
FATAL
GETNUMB
VERSION
GETTEXT
GETWORD
TRIMTEXT
189
TINKERUser'sGuide
GETTEXT
LATTICE
SUFFIX
189
READXYZ
CHKXYZ
FATAL
SORT
GETTEXT
TRIMTEXT
GETWORD
VERSION
NEXTTEXT
REFINE
LBFGS
REPLICA
FATAL
RGDSRCH
CLIMBRGD
EIGENRGD
RIGIDXYZ
RGDSTEP
CHOLESKY
GRADIENT
MDSTAT
KINETIC
PRESSURE
LINBODY
ROTRGD
MDSAVE
TEMPER2
RIBOSOME
ADDBOND
ADDSIDE
NEWATM
FATAL
OLDATM
FINDATM
PRTSEQ
FREEUNIT
VERSION
RINGS
ANGLES
BITORS
BONDS
FATAL
TORSIONS
RMSERROR
TRIMTEXT
ROTANG
DOT
ROTCHECK
ROTLIST
ROTLIST
FATAL
ROTPOLE
ROTMAT
ROTSITE
SADDLE
COMMENT'
FATAL
GETXYZ
MAKEXYZ
PATHSCAN
SADDLE1
VERSION
FINAL
IMPOSE
MECHANIC
PATHVAL
SEARCH
FREEUNIT
INITIAL
NEXTARG
PRTXYZ
TANGENT
GETTEXT
MAKEINT
PATHPNT
READXYZ
UPCASE
SADDLE1
GRADIENT
SADDLES
CERROR
IPEDGE
TRIPLE
SCAN
ACTIVE
FINAL
INITROT
MECHANIC
READXYZ
FREEUNIT
LOCALMIN
MODESRCH
VERSION
GETXYZ
MAKEINT
NEXTARG
INITIAL
MAPCHECK
NUMERAL
SCAN1
GRADIENT
SCAN2
HESSIAN
SDAREA
SURFATOM
190
VCROSS
TINKERUser'sGuide
190
SDSTEP
GRADIENT
KINETIC
RATTLE
SDTERM
NORMAL
SDAREA
SETIME
CLOCK
SHAKEUP
CHKRING
SKTDYN
CREATEUPDATE
GETMONITOR
RELEASEMONITOR
SETCOORDINATES
SETINDUCED SETVELOCITY SKTINIT
SKTINIT
CREATEJVM
CREATESERVERCREATESYSTEMSETATOMIC
SETATOMTYPESSETCHARGE
SETCONNECTIVITY
SETCOORDINATES
SETFILE
SETFORCEFIELD
SETKEYWORD
SETMASS
SETNAME
SETSTORY
SKTKILL
DESTROYJVM
DESTROYSERVER
SKTOPT
CREATEUPDATE
GETMONITOR
RELEASEMONITOR
SETENERGY
SETSTEP
SETUPDATED
NEEDUPDATE
SETCOORDINATES
SETGRADIENTS SETINDUCED
SKTINIT
SLATER
ASET
BSET
CJKM
POLYP
SMOOTH
GETTEXT
GETWORD
NEXTARG
UPCASE
SNIFFER
FINAL
FREEUNIT
INITIAL
OPTSAVE
GETREF
MAKEREF
PRTXYZ
GETXYZ
MECHANIC
SNIFFER1
GRADIENT
NEXTARG
VERSION
SNIFFER1
GRADIENT
SOAK
DELETE
FREEUNIT
MERGE
UNITCELL
IMAGE
MOLECULE
VERSION
LATTICE
READXYZ
MAKEREF
SUFFIX
SPACEFILL
ACTIVE
CONNOLLY
GETTEXT
KVDW
UPCASE
FIELD
GETXYZ
NEXTARG
VERSION
FINAL
INITIAL
READXYZ
FREEUNIT
KATOM
SUFFIX
SPECTRUM
BASEFILE
FREEUNIT
VERSION
INITIAL
NEXTARG
SUFFIX
191
GETNUMB
MDSAVE
RATTLE2
MDSTAT
SDTERM
PRESSURE
GETTEXT
GETWORD
UPCASE
TINKERUser'sGuide
NEEDUPDATE
SETACCELERATION
SETENERGY
SETTIME
SETUPDATED
SKTDYN
SKTOPT
191
SQUARE
GETTEXT
LMSTEP
RSDVALUE
LSQWRITE
TRUST
PRECISE
UPCASE
QRFACT
SUFFIX
TRIMTEXT
SUPERPOSE
FIELD
FINAL
IMPOSE
PRTXYZ
UPCASE
FREEUNIT
INITIAL
READXYZ
VERSION
GETTEXT
KATOM
SUFFIX
GETXYZ
NEXTARG
TRIMTEXT
SURFACE
FATAL
SORT2
SURFATOM
FATAL
SORT2
SWITCH
REPLICA
SYBYLXYZ
FINAL
GETMOL2
INITIAL
PRTXYZ
SYMMETRY
CELLATOM
TANGENT
PATHPNT
TEMPER
KINETIC
TEMPER2
MAXWELL
RANDOM
RANVEC
TESTGRAD
ENERGY
FINAL
INITIAL
GETTEXT
MECHANIC
GETXYZ
NEXTARG
GRADIENT
UPCASE
TESTHESS
FINAL
FREEUNIT
HESSIAN
NUMGRAD
GETTEXT
INITIAL
UPCASE
GETXYZ
MECHANIC
VERSION
GRADIENT
NEXTARG
TESTLIGHT
EBUCK
EBUCK1
EGAUSS1
EMM3HB
GETXYZ
NEXTARG
ECHARGE
EHAL
EMM3HB1
INITIAL
SETIME
ECHARGE1
EHAL1
FINAL
LIGHTS
EGAUSS
ELJ ELJ1
GETIME
MECHANIC
TESTROT
ENERGY
FINAL
INITROT
GETINT
MAKEXYZ
GRADROT
MECHANIC
INITIAL
NEXTARG
TIMER
ENERGY
FINAL
GRADIENT
NEXTARG
GETIME
HESSIAN
SETIME
GETTEXT
INITIAL
UPCASE
GETXYZ
MECHANIC
TIMEROT
ENERGY
FINAL
GRADROT
MECHANIC
GETIME
HESSROT
NEXTARG
GETINT
INITIAL
SETIME
GETTEXT
INITROT
UPCASE
192
FREEUNIT
VERSION
SADDLE1
TINKERUser'sGuide
192
TNCG
GETTEXT
TNSOLVE
PRECOND
TORSIONS
FATAL
TORUS
CERROR
GETTOR
TOTERR
BNDERR
CHIRER
TRIANGLE
FATAL
TRIPLE
DOT
VCROSS
TRUST
PRECISE
RSDVALUE
UDIRECT2
ERFC
IMAGE
SWITCH
UMUTUAL2
ERFC
IMAGE
SWITCH
UNITCELL
FATAL
GETTEXT
GETWORD
UPCASE
VAM
CERROR
CIRPLN
GENDOT
MEASPM
DEPTH
MEASFN
TRIPLE
DIST2
MEASFP
VCROSS
DOT
MEASFS
VNORM
VDWERR
LIGHTS
VECANG
ANORM
DOT
TRIPLE
VERLET
GRADIENT
KINETIC
RATTLE
MDSAVE
RATTLE2
MDSTAT
TEMPER
PRESSURE
TEMPER2
VERSION
LOWCASE
NEXTARG
TRIMTEXT
VIBRATE
DIAGQ
FATAL
HESSIAN
NUMERAL
FINAL
INITIAL
PRTXYZ
FREEUNIT
MECHANIC
VERSION
GETXYZ
NEXTARG
VIBRIGID
DIAGQ
FINAL
MECHANIC
GETXYZ
ORIENT
HESSRGD
INITIAL
VIBROT
DIAGQ
FINAL
INITROT
GETINT
MECHANIC
HESSROT
INITIAL
VNORM
ANORM
193
HMATRIX
TNSOLVE
OPTSAVE
UPCASE
PISCF
SEARCH
LOCERR
TORSER
VDWERR
TINKERUser'sGuide
193
VOLUME
CONNOLLY
VOLUME1
FATAL
VOLUME2
FATAL
WATSON
ZATOM
WATSON1
GRADRGD
RIGIDXYZ
XTALERR
ENERGY
XTALMOVE
XTALPRM
XTALFIT
FINAL
GETXYZ
POTOFF
INITIAL
SQUARE
MECHANIC
XTALPRM
NEXTARG
XTALLAT1
ENERGY
LATTICE
XTALMIN
FINAL
FREEUNIT
LATTICE
TNCG
GETXYZ
MECHANIC
VERSION
GRADIENT
NEXTARG
XTALLAT1
INITIAL
OCVMPRTXYZ
XTALMOL1
GRADIENT
XTALMOL2
HESSIAN
XTALMOVE
LATTICE
XTALPRM
BOUNDS
LATTICE
MOLECULE
XYZEDIT
ACTIVE
BOUNDS
FREEUNIT
INITIAL
MAKEREF
RANDOM
UNITCELL
CUTOFFS
GETXYZ
INSERT
MERGE
SOAK
VERSION
DELETE
IMAGE
KATOM
MOLECULE
SORT
FIELDFINAL
INERTIA
LATTICE
PRTXYZ
SORT4
XYZINT
FINAL
FREEUNIT
MAKEINT
UPCASE
GETTEXT
NEXTARG
VERSION
GETXYZ
PRTINT
INITIAL
READINT
XYZPDB
FIELD
FINAL
KATOM
VERSION
FREEUNIT
MAKEPDB
GETXYZ
MOLECULE
INITIAL
PRTPDB
XYZRIGID
JACOBI
ROTEULER
XYZSYBYL
BONDS
FINAL
PRTMOL2
FREEUNIT
VERSION
GETXYZ
INITIAL
ZATOM
FATAL
194
TINKERUser'sGuide
194
ZVALUE
195
MAKEXYZ
TRIMTEXT
TINKERUser'sGuide
195
12.
TestCases&Examples
This section contains brief descriptions of the sample calculations found in the EXAMPLE
subdirectory of the TINKER distribution. These examples exercise several of the current TINKER
programsandareintendedtoprovideaflavorofthecapabilitiesofthepackage.
ANIONExample
ComputesanestimationofthefreeenergyofhydrationofCl-anionvs.Br-anionviaa2picosecond
simulationona``hybrid''anioninaboxofwaterfollowedbyafreeenergyperturbationcalculation
ARGONExample
Performsaninitialenergyminimizationonaperiodicboxcontaining150argonatomsfollowedby6
picoseconds of a molecular dynamics using a modified Beeman integration algorithm and a
Bersedsenthermostat
CLUSTERExample
Performs a set of 10 Gaussian density annealing (GDA) trials on a cluster of 13 argon atoms in an
attempttolocatetheglobalminimumenergystructure
CRAMBINExample
Generates a TINKER file from a PDB file, followed by a single point energy computation and
determinationofthemolecularvolumeandsurfacearea
CYCLOHEXExample
First approximately locates the transition state between chair and boat cyclohexane, followed by
subsequent refinement of the transition state and a final vibrational analysis to show that a single
negativefrequencyisassociatedwiththesaddlepoint
DIALANINEExample
Findsallthelocalminimaofalaninedipeptideviaapotentialenergysurfacescanusingtorsional
modestojumpbetweentheminima
ENKEPHALINExample
Producescoordinatesfromthemet-enkephalinaminoacidsequenceandphi/psiangles,followedby
truncatedNewtonenergyminimizationanddeterminationofthelowestfrequencynormalmode
FORMAMIDEExample
Convertstoaunitcellfromfractionalcoordinates,followedbyfullcrystalenergyminimizationand
determination of optimal carbonyl oxygen energy parameters from a fit to lattice energy and
structure
196
TINKERUser'sGuide
196
HELIXExample
Performsarigid-bodyoptimizationofthepackingoftwoidealizedpolyalaninehelicesusingonlyvan
derWaalsinteractions
SALTExample
Converts a sodium chloride assymetric unit to the corresponding unit cell, then runs a crystal
minimization starting from the initial diffraction structure using Ewald summation to model the
long-rangeelectrostaticinteractions.
197
TINKERUser'sGuide
197
13.
BenchmarkResults
The tables in this section provide CPU benchmarks for basic TINKER energy and derivative
evaluations, vibrational analysis and molecular dynamics. All times are in seconds and were
measuredwithTINKERexecutablesdimensionedtomaxatmof10000andmaxhessof1000000in
thesourcefilesizes.i.Allcalculationswereruntwiceinrapidsuccessiononaquietmachine.The
timesreportedforeachbenchmarkaretheresultsfromthesecondrun.IfyouhavebuiltTINKERon
an alternative machine type and are able to run the benchmarks on the additional machine type,
pleasesendtheresultsforinclusioninafuturelisting.
BENCHMARK#1:CalmodulinEnergyEvaluation
Thesystemisanisolatedmoleculeofthe148-residueproteincalmodulinwith2264atomsusingthe
Amber ff94 force field. All interactions are computed with no use of cutoffs. Times listed are for
calculationsetupfollowedbyasingleenergy,energy/gradientandHessianevaluation.
MACHINE-OS-COMPILERTYPE
MHz
AthlonXP2400+(RH8.0,Intel)
AthlonXP2400+(RH8.0,PGI)
AthlonXP2400+(RH8.0,g773.2)
AthlonThunderbird(RH8.0,Intel)
AthlonThunderbird(RH8.0,PGI)
AthlonThunderbird(RH8.0,g773.2)
AthlonClassic(RH8.0,Intel)
AthlonClassic(RH8.0,PGI)
AthlonClassic(RH8.0,g773.2)
CompaqEvoN610cP4(RH8.0,Intel)
CompaqEvoN610cP4(RH8.0,PGI)
CompaqEvoN610cP4(RH8.0,Absoft)
CompaqEvoN610cP4(RH8.0,g773.2)
CompaqEvoN610cP4(WinXP,CVF6.6)
CompaqEvoN610cP4(WinXP,g773.2)
ApplePowerMacG4(OSX10.2,Absoft)
ApplePowerMacG4(OSX10.2,g773.3)
CompaqAlphaServerDS10(Tru645.0)
SGIIndigoIIR10K(Irix6.5,MIPS)
2000
2000
2000
1400
1400
1400
950
950
950
2000
2000
2000
2000
2000
2000
733
733
466
195
SETUP
0.13
0.16
0.17
0.22
0.21
0.19
0.30
0.30
0.31
0.18
0.22
0.17
0.19
0.16
0.16
0.41
0.37
0.35
1.17
ENERGY
GRAD
HESS
0.60
0.70
0.66
0.86
1.00
0.94
1.42
1.65
1.57
0.87
1.06
1.06
1.07
0.98
1.08
5.12
3.79
1.93
6.35
2.96
3.60
3.67
5.15
5.92
5.81
7.07
7.96
7.94
3.08
4.27
3.95
4.41
3.54
4.45
17.83
14.48
8.40
23.03
0.28
0.31
0.28
0.41
0.44
0.40
0.64
0.69
0.63
0.45
0.44
0.52
0.41
0.38
0.40
2.96
1.98
1.33
3.49
BENCHMARK#2:CrambinCrystalEnergyEvaluation
Thesystemisaunitcellofthe46-residueproteincrambincontaining2polypeptidechains,2ethanol
and178watermoleculesforatotalof1360atomsusingtheOPLS-UAforcefield.Periodicboundaries
areusedwithparticlemeshEwaldforelectrostaticsanda9.0≈cutoffforvdWinteractions.Times
listedareforcalculationsetupfollowedbyasingleenergy,energy/gradientandHessianevaluation.
MACHINE-OS-COMPILERTYPE
AthlonXP2400+(RH8.0,Intel)
AthlonXP2400+(RH8.0,PGI)
198
MHz
2000
2000
SETUP
0.12
0.13
TINKERUser'sGuide
ENERGY
0.12
0.14
GRAD
HESS
0.21
0.24
0.66
0.63
198
AthlonXP2400+(RH8.0,g773.2)
AthlonThunderbird(RH8.0,Intel)
AthlonThunderbird(RH8.0,PGI)
AthlonThunderbird(RH8.0,g773.2)
AthlonClassic(RH8.0,Intel)
AthlonClassic(RH8.0,PGI)
AthlonClassic(RH8.0,g773.2)
CompaqEvoN610cP4(RH8.0,Intel)
CompaqEvoN610cP4(RH8.0,PGI)
CompaqEvoN610cP4(RH8.0,Absoft)
CompaqEvoN610cP4(RH8.0,g773.2)
CompaqEvoN610cP4(WinXP,CVF6.6)
CompaqEvoN610cP4(WinXP,g773.2)
ApplePowerMacG4(OSX10.2,Absoft)
ApplePowerMacG4(OSX10.2,g773.3)
CompaqAlphaServerDS10(Tru645.0)
SGIIndigoIIR10K(Irix6.5,MIPS)
2000
1400
1400
1400
950
950
950
2000
2000
2000
2000
2000
2000
733
733
466
195
0.14
0.19
0.18
0.17
0.26
0.29
0.27
0.15
0.22
0.14
0.15
0.14
0.12
0.32
0.31
0.29
0.92
0.13
0.17
0.18
0.17
0.25
0.27
0.27
0.14
0.19
0.22
0.20
0.17
0.22
0.58
0.42
0.38
0.74
0.28
0.30
0.32
0.38
0.47
0.50
0.56
0.27
0.33
0.39
0.45
0.33
0.52
1.09
0.79
0.64
1.41
0.81
0.91
0.91
1.11
1.46
1.42
1.70
0.64
0.88
0.84
1.13
0.83
1.16
3.11
2.37
1.95
3.89
BENCHMARK#3:PeptideNormalModeCalculation
Thesystemisaminimumenergyconformationofa20-residuepeptidecontainingoneofeachofthe
standardaminoacidsforatotalof328atomsusingtheOPLS-AAforcefieldwithoutcutoffs.Thetime
reportedisforcomputationoftheHessianandcalculationofthenormalmodesoftheHessianmatrix
andthevibrationfrequenciesrequiringtwoseparatematrixdiagonalizationsteps.
MACHINE-OS-COMPILERTYPE
MHz
AthlonXP2400+(RH8.0,Intel)
AthlonXP2400+(RH8.0,PGI)
AthlonXP2400+(RH8.0,g773.2)
AthlonThunderbird(RH8.0,Intel)
AthlonThunderbird(RH8.0,PGI)
AthlonThunderbird(RH8.0,g773.2)
AthlonClassic(RH8.0,Intel)
AthlonClassic(RH8.0,PGI)
AthlonClassic(RH8.0,g773.2)
CompaqEvoN610cP4(RH8.0,Intel)
CompaqEvoN610cP4(RH8.0,PGI)
CompaqEvoN610cP4(RH8.0,Absoft)
CompaqEvoN610cP4(RH8.0,g773.2)
CompaqEvoN610cP4(WinXP,CVF6.6)
CompaqEvoN610cP4(WinXP,g773.2)
ApplePowerMacG4(OSX10.2,Absoft)
ApplePowerMacG4(OSX10.2,g773.3)
CompaqAlphaServerDS10(Tru645.0)
SGIIndigoIIR10K(Irix6.5,MIPS)
2000
2000
2000
1400
1400
1400
950
950
950
2000
2000
2000
2000
2000
2000
733
733
466
195
NORMALMODES
22
26
24
31
34
33
46
51
48
19
19
20
19
19
20
67
62
39
144
BENCHMARK#4:TIP3PWaterBoxMolecularDynamics
199
TINKERUser'sGuide
199
The system consists of 216 rigid TIP3P water molecules in a 18.643 ≈ periodic box, 9.0 ≈ shifted
energyswitchcutoffsfornonbondedinteractions.Thetimereportedisfor1000dynamicsstepsof
1.0fseachusingthemodifiedBeemanintegratorandRattleconstraintsonallbondlengths.
MACHINE-OS-COMPILERTYPE
MHz
AthlonXP2400+(RH8.0,Intel)
AthlonXP2400+(RH8.0,PGI)
AthlonXP2400+(RH8.0,g773.2)
AthlonThunderbird(RH8.0,Intel)
AthlonThunderbird(RH8.0,PGI)
AthlonThunderbird(RH8.0,g773.2)
AthlonClassic(RH8.0,Intel)
AthlonClassic(RH8.0,PGI)
AthlonClassic(RH8.0,g773.2)
CompaqEvoN610cP4(RH8.0,Intel)
CompaqEvoN610cP4(RH8.0,PGI)
CompaqEvoN610cP4(RH8.0,Absoft)
CompaqEvoN610cP4(RH8.0,g773.2)
CompaqEvoN610cP4(WinXP,CVF6.6)
CompaqEvoN610cP4(WinXP,g773.2)
ApplePowerMacG4(OSX10.2,Absoft)
ApplePowerMacG4(OSX10.2,g773.3)
CompaqAlphaServerDS10(Tru645.0)
SGIIndigoIIR10K(Irix6.5,MIPS)
2000
2000
2000
1400
1400
1400
950
950
950
2000
2000
2000
2000
2000
2000
733
733
466
195
DYNAMICS
37
34
45
52
47
63
77
71
96
53
54
55
91
63
94
209
170
106
280
BENCHMARK#5:TINKERWaterBoxMolecularDynamics
The system consists of 216 AMOEBA flexible polarizable atomic multipole water molecules in a
18.643 ≈ periodic box using regular Ewald summation for the electrostatics and a 12.0 ≈ switched
cutoff for vdW interactions. The time reported is for 100 dynamics steps of 1.0 fs each using the
modifiedBeemanintegratorand0.01Debyermsconvergenceforinduceddipolemoments.
MACHINE-OS-COMPILERTYPE
MHz
AthlonXP2400+(RH8.0,Intel)
AthlonXP2400+(RH8.0,PGI)
AthlonXP2400+(RH8.0,g773.2)
AthlonThunderbird(RH8.0,Intel)
AthlonThunderbird(RH8.0,PGI)
AthlonThunderbird(RH8.0,g773.2)
AthlonClassic(RH8.0,Intel)
AthlonClassic(RH8.0,PGI)
AthlonClassic(RH8.0,g773.2)
CompaqEvoN610cP4(RH8.0,Intel)
CompaqEvoN610cP4(RH8.0,PGI)
CompaqEvoN610cP4(RH8.0,Absoft)
CompaqEvoN610cP4(RH8.0,g773.2)
CompaqEvoN610cP4(WinXP,CVF6.6)
CompaqEvoN610cP4(WinXP,g773.2)
ApplePowerMacG4(OSX10.2,Absoft)
200
2000
2000
2000
1400
1400
1400
950
950
950
2000
2000
2000
2000
2000
2000
733
TINKERUser'sGuide
DYNAMICS
108
104
128
165
158
183
282
261
307
156
191
226
243
176
263
680
200
ApplePowerMacG4(OSX10.2,g773.3)
CompaqAlphaServerDS10(Tru645.0)
SGIIndigoIIR10K(Irix6.5,MIPS)
201
733
466
195
TINKERUser'sGuide
479
358
868
201
14.
Collaborators&Acknowledgments
TheTINKERpackagehasdevelopedoveraperiodofmanyyears,veryslowlyduringthelate-1980s,
andmorerapidlysincethemid-1990sinJayPonder'sresearchgroupattheWashingtonUniversity
School of Medicine in Saint Louis. Many people have played significant roles in the development of
thepackageintoitscurrentform.Themajorcontributorsarelistedbelow:
StewRubenstein
coordinateinterconversions;originaloptimizationmethods
andtorsionalanglemanipulation
CraigKundrot
molecularsurfacearea&volumeandtheirderivatives
ShawnHuston
originalAMBER/OPLSimplementation;freeenergy
calculations;timecorrelationfunctions
MikeDudek
initialmultipolemodelsforpeptidesandproteins
Yong"Mike"Kong
multipoleelectrostatics;dipolepolarization;reactionfield
treatment;TINKERwatermodel
ReeceHart
potentialsmoothingmethodology;Scheraga'sDEM,
Straub'sGDAandextensions
MikeHodsdon
extensionoftheTINKERdistgeomprogramandits
applicationtoNMRNOEstructuredetermination
RohitPappu
potentialsmoothingmethodologyandPSSalgorithms;
rigidbodyoptimization;GB/SAsolvationderivatives
WijnandMooij
MM3directionalhydrogenbondingterm;crystallattice
minimizationcode
GeraldLoeffler
stochastic/Langevindynamicsimplementation
MarinaVorobieva
NinaSokolova
nucleicacidbuildingmoduleandparametertranslation
PeterBagossi
AMOEBAforcefieldparametersforalkanesanddiatomics
PengyuRen
Ewaldsummationforpolarizableatomicmultipoles;
AMOEBAforcefieldforwater,organicsandpeptides
AndersCarlsson
originalligandfieldpotentialenergytermfortransitionmetals
AndreyKutepov
integratorforrigid-bodydynamicstrajectories
TomDarden
ParticleMeshEwald(PME)code,anddevelopmentofPME
fortheAMOEBAforcefield
202
TINKERUser'sGuide
202
AlanGrossfield
MonteCarlominimization;tophatpotentialsmoothing
MichaelSchnieders
ForceFieldExplorerGUIforTINKER;neighborlistsfor
nonbondedinteractions
ChuanjieWu
JustinXiang
DavidGohara
solvationfreeenergycalculations;AMOEBAnucleicacidforce
field;parameterizationtoolsforTINKER
angularoverlapandvalencebondpotentialmodelsfor
transitionmetals
OpenMPparallelizationofenergytermsincludingPME,
andparallelneighborlists
It is critically important that TINKER's distributed force field parameter sets exactly reproduce the
intent of the original force field authors. We would like to thank Julian Tirado-Rives (OPLS-AA),
Alex MacKerell (CHARMM27), Wilfred van Gunsteren (GROMOS), and Adrian Roitberg and
Carlos Simmerling (AMBER) for their help in testing TINKER's results against those given by the
authentic programs and parameter sets. Lou Allinger provided updated parameters for MM2 and
MM3 on several occasions. His very successful methods provided the original inspiration for the
developmentofTINKER.
Still other workers have devoted considerable time in developing code that will hopefully be
incorporated into future TINKER versions; for example, Jim Kress (UFF implementation) and
Michael Sheets (numerous code optimizations, thermodynamic integration). Finally, we wish to
thank the many users of the TINKER package for their suggestions and comments, praise and
criticism,whichhaveresultedinavarietyofimprovements.
203
TINKERUser'sGuide
203
15.
References&SuggestedReading
Thissectioncontainsalistofthereferencestogeneraltheory,algorithmsandimplementationdetails
whichhavebeenofuseduringthedevelopmentoftheTINKERpackage.Methodsdescribedinsome
ofthereferenceshavebeenimplementedindetailwithintheTINKERsourcecode.Otherreferences
contain useful background information although the algorithms themselves are now obsolete. Still
other papers contain ideas or extensions planned for future inclusion in TINKER. References for
specificforcefieldparametersetsareprovidedinanearliersectionofthisUser'sGuide.Thislistis
heavily skewed toward biomolecules in general and proteins in particular. This bias reflects our
group's major interests; however an attempt has been made to include methods which should be
generallyapplicable.
PARTIALLISTOFMOLECULARMECHANICSSOFTWAREPACKAGES
AMBER
AMMP
ARGOS
BOSS
BRUGEL
CFF
CHARMM
CHARMM/GEMM
DELPHI
DISCOVER
DL_POLY
ECEPP
ENCAD
FANTOM
FEDER/2
GROMACS
GROMOS
IMPACT
MACROMODEL
MM2/MM3/MM4
MMC
MMFF
MMTK
MOIL
MOLARIS
MOLDY
MOSCITO
NAMD
OOMPAA
ORAL
ORIENT
PCMODEL
PEFF
Q
SIBFA
SIGMA
SPASIBA
SPASMS
204
PeterKollman,UniversityofCalifornia,SanFrancisco
RobHarrison,ThomasJeffersonUniversity,Philadelphia
AndyMcCammon,UniversityofCalifornia,SanDiego
WilliamJorgensen,YaleUniversity
ShoshonaWodak,FreeUniversityofBrussels
ShneiorLifson,WeizmannInstitute
MartinKarplus,HarvardUniversity
BernardBrooks,NationalInstitutesofHealth,Bethesda
BastianvandeGraaf,DelftUniversityofTechnology
MolecularSimulationsInc.,SanDiego
W.Smith&T.Forester,CCP5,DaresburyLaboratory
HaroldScheraga,CornellUniversity
MichaelLevitt,StanfordUniversity
WernerBraun,UniversityofTexas,Galveston
NobuhiroGo,KyotoUniversity
HermanBerendsen,UniversityofGroningen
WilfredvanGunsteren,BIOMOSandETH,Zurich
RonaldLevy,RutgersUniversity
Schodinger,Inc.,JerseyCity,NewJersey
N.LouAllinger,UniversityofGeorgia
CliffDykstra,IndianaUniv.≠PurdueUniv.atIndianapolis
TomHalgren,MerckResearchLaboratories,Rahway
KonradHinsen,Inst.ofStructuralBiology,Grenoble
RonElber,CornellUniversity
AriehWarshal,UniversityofSouthernCalifornia
KeithRefson,OxfordUniversity
DietmarPaschek&AlfonsGeiger,Universit‰tDortmund
KlausSchulten,UniversityofIllinois,Urbana
AndyMcCammon,UniversityofCalifornia,SanDiego
KarelZimmerman,INRA,Jouy-en-Josas,France
AnthonyStone,CambridgeUniversity
KevinGilbert,SerenaSoftware,Bloomington,Indiana
JanDillen,UniversityofPretoria,SouthAfrica
Johan≈qvist,UppsalaUniversity
NohadGresh,INSERM,CNRS,Paris
JanHermans,UniversityofNorthCarolina
GerardVergoten,UniversitÈdeLille
DavidSpellmeyerandtheKollmanGroup,UCSF
TINKERUser'sGuide
204
TINKER
XPLOR/CNS
YAMMP
YASP
YETI
JayPonder,WashingtonUniversity,St.Louis
AxelBr¸nger,StanfordUniversity
StephenHarvey,UniversityofAlabama,Birmingham
FlorianMueller-Plathe,ETHZentrum,Zurich
AngeloVedani,Biografik-Labor3R,Basel
AMBER D. A Pearlman, D. A. Case, J. W. Caldwell, W. S. Ross, T. E. Cheatham III, S. DeBolt, D.
Ferguson,G.SeibelandP.Kollman,AMBER,aPackageofComputerProgramsforApplyingMolecular
Mechanics,NormalModeAnalysis,MolecularDynamicsandFreeEnergyCalculationstoSimulatethe
StructuralandEnergeticPropertiesofMolecules,Comp.Phys.Commun.,91,1-41(1995)
ARGOS T. P. Straatsma and J. A. McCammon, ARGOS, a Vectorized General Molecular Dynamics
Program,J.Comput.Chem.,11,943-951(1990)
CHARMMB.R.Brooks,R.E.Bruccoleri,B.D.Olafson,D.J.States,S.SwaminathanandM.Karplus,
CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations, J.
Comput.Chem.,4,187-217(1983)
ENCAD M. Levitt, M. Hirshberg, R. Sharon and V. Daggett, Potential Energy Function and
Parameters for Simulations for the Molecular Dynamics of Proteins and Nucleic Acids in Solution,
Comp.Phys.Commun.,91,215-231(1995)
FANTOMT.Schaumann,W.BraunandK.Wurtrich,TheProgramFANTOMforEnergyRefinement
of Polypeptides and Proteins Using a Newton-Raphson Minimizer in Torsion Angle Space,
Biopolymers,29,679-694(1990)
FEDER/2 H. Wako, S. Endo, K. Nagayama and N. Go, FEDER/2: Program for Static and Dynamic
ConformationalEnergyAnalysisofMacro-moleculesinDihedralAngleSpace,Comp.Phys.Commun.,
91,233-251(1995)
GROMACS E. Lindahl, B. Hess and D. van der Spoel, GROMACS 3.0: A Package for Molecular
SimulationandTrajectoryAnalysis,J.Mol.Mol.,7,306-317(2001)
GROMOSW.R.P.Scott,P.H.Hunenberger,I.G.Tironi,A.E.Mark,S.R.Billeter,J.Fennen,A.E.
Torda, T. Huber, P. Kruger, W. F. van Gunsteren, The GROMOS Biomolecular Simulation Program
Package,J.Phys.Chem.A,103,3596-3607(1999)
IMPACT D. B. Kitchen, F. Hirata, J. D. Westbrook, R. Levy, D. Kofke and M. Yarmush, Conserving
EnergyduringMolecularDynamicsSimulationsofWater,Proteins,andProteinsinWater,J.Comput.
Chem.,10,1169-1180(1990)
MACROMODELF.Mahamadi,N.G.J.Richards,W.C.Guida,R.Liskamp,M.Lipton,C.Caufield,G.
Chang, T. Hendrickson and W. C. Still, MacroModel≠An Integrated Software System for Modeling
OrganicandBioorganicMoleculesUsingMolecularMechanics,J.Comput.Chem.,11,440-467(1990)
MM2 N. L. Allinger, Conformational Analysis. 130. MM2. A Hydrocarbon Force Field Utilizing V1
andV2TorsionalTerms,J.Am.Chem.Soc.,99,8127-8134(1977)
MM3 N. L. Allinger, Y. H. Yuh and J.-H. Lii, Molecular Mechanics. The MM3 Force Field for
Hydrocarbons,J.Am.Chem.Soc.,111,8551-8566(1989)
205
TINKERUser'sGuide
205
MM4 N. L. Allinger, K. Chen and J.-H. Lii, An Improved Force Field (MM4) for Saturated
Hydrocarbons,J.Comput.Chem.,17,642-668(1996)
MMCC.E.Dykstra,MolecularMechanicsforWeaklyInteractingAssembliesofRareGasAtomsand
SmallMolecules,J.Am.Chem.Soc.,111,6168-6174(1989)
MMFF T. A. Halgren, Merck Molecular Force Field. I. Basis, Form, Scope, Parameterization, and
PerformanceofMMFF94,J.Comput.Chem.,17,490-516(1996)
MOILR.Elber,A.Roitberg,C.Simmerling,R.Goldstein,H.Li,G.Verkhiver,C.Keasar,J.ZhangandA.
Ulitsky, MOIL: A Program for Simulations of Macromolecules, Comp. Phys. Commun., 91, 159-189
(1995)
MOSCITOSeethewebsiteathttp:/ganter.chemie.uni-dortmund.de/~pas/moscito.html
NAMDL.KalÈ,R.Skeel,M.Bhandarkar,R.Brunner,A.Gursoy,N.Krawetz,J.Phillips,A.Shinozaki,
K. Varadarajan and K. Schulten, NAMD2: Greater Scalability for Parallel Molecular Dynamics, J.
Comput.Phys.,151,283-312(1999)
OOMPAA G. A. Huber and J. A. McCammon, OOMPAA≠Object-oriented Model for Probing
AssemblagesofAtoms,J.Comput.Phys.,151,264-282(1999)
ORALK.Zimmermann,ORAL:AllPurposeMolecularMechanicsSimulatorandEnergyMinimizer,J.
Comput.Chem.,12,310-319(1991)
PCMODELSeethewebsiteathttp:/www.serenasoft.com
PEFF J. L. M. Dillen, PEFF: A Program for the Development of Empirical Force Fields,J. Comput.
Chem.,13,257-267(1992)
QSeethewebsiteathttp://aqvist.bmc.uu.se/Q
SIBFAN.Gresh,Inter-andIntramolecularInteractions.InceptionandRefinementsoftheSIBFA,
MolecularMechanics(SMM)Procedure,aSeparable,PolarizableMethodologyGroundedonabInitio
SCF/MP2Computations.ExamplesofApplicationstoMolecularRecognitionProblems,J.Chim.Phys.
PCB,94,1365-1416(1997)
SIGMASeethewebsiteathttp://femto.med.unc.edu/SIGMA
SPASIBAP.DerreumauxandG.Vergoten,ANewSpectroscopicMolecularMechanicsForce-Field-
ParametersForProteins,J.Chem.Phys.,102,8586-8605(1995)
TINKERSeethewebsiteathttp://dasher.wustl.edu/tinker
YAMMP R. K.-Z. Tan and S. C. Harvey, Yammp: Development of a Molecular Mechanics Program
UsingtheModularProgrammingMethod,J.Comput.Chem.,14,455-470(1993)
YETI A. Vedani, YETI: An Interactive Molecular Mechanics Program for Small-Molecule Protein
Complexes,J.Comput.Chem.,9,269-280(1988)
206
TINKERUser'sGuide
206
MOLECULARMECHANICS
U. Burkert and N. L. Allinger, Molecular Mechanics, American Chemical Society, Washington, D.C.,
1982
P.CombaandT.W.Hambley,MolecularModelingofInorganicCompounds,2ndEd.,Wiley-VCH,
NewYork,2001
K. Machida, Principles of Molecular Mechanics, Kodansha/John Wiley & Sons, Tokyo/New York,
1999
A. K. RappÈ and C. J. Casewit, Molecular Mechanics across Chemistry, University Science Books,
Sausalito,CA,1997
K. Rasmussen, Potential Energy Functions in Conformational Analysis (Lecture Notes in
Chemistry,Vol.27),Springer-Verlag,Berlin,1985
COMPUTERSIMULATIONMETHODS
M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids, Oxford University Press, Oxford,
1987
C.J.Cramer,EssentialsofComputationalChemistry:TheoriesandModels,JohnWileyandSons,
NewYork,2002
M. J. Field, A Practical Introduction to the Simulation of Molecular Systems, Cambridge Univ.
Press,Cambridge,1999
D.FrankelandB.Smit,UnderstandingMolecularSimulation:FromAlgorithmstoApplications,
2ndEd.,AcademicPress,SanDiego,CA,2001
J.M.Haile,MolecularDynamicsSimulation:ElementaryMethods,JohnWileyandSons,NewYork,
1992
F.Jensen,IntroductiontoComputationalChemistry,JohnWileyandSons,NewYork,1998
A.R.Leach,MolecularModelling:PrinciplesandApplications,2ndEd.,AddisonWesleyLongman,
Essex,England,2001
D.C.Rapaport,TheArtofMolecularDynamicsSimulation,2ndEd.,CambridgeUniversityPress,
Cambridge,2004
T.Schlick,MolecularModelingandSimulation,Springer-Verlag,NewYork,2002
MODELINGOFBIOLOGICALMACROMOLECULES
O.M.Becker,A.D.MacKerell,Jr.,B.RouxandM.Watanabe,Eds.,ComputationalBiochemistryand
Biophysics,MarcelDekker,NewYork,2001
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TINKERUser'sGuide
207
C. L. Brooks III, M. Karplus and B. M. Pettitt, Proteins: A Theoretical Perspective of Dynamics,
Structure,andThermodynamics,JohnWileyandSons,NewYork,1988
V. Daggett, Ed., Protein Simulations (Advances in Protein Chemistry, Vol. 66), Academic
Press/Elsevier,NewYork,2003
J. A. McCammon and S. Harvey, Dynamics of Proteins and Nucleic Acids, Cambridge University
Press,Cambridge,1987
W. F. van Gunsteren, P. K. Weiner and A. J. Wilkinson, Computer Simulation of Biomolecular
Systems,Vol.1-3,KluwerAcademicPublishers,Dordrecht,1989-1997
CONJUGATEGRADIENTANDQUASI-NEWTONOPTIMIZATION
J.NocedalandS.J.Wright,NumericalOptimization,Springer-Verlag,NewYork,1999
S.G.NashandA.Sofer,LinearandNonlinearProgramming,McGraw-Hill,NewYork,1996
R.Fletcher,PracticalMethodsofOptimization,JohnWiley&SonsLtd.,Chichester,1987
D. G. Luenberger, Linear and Nonlinear Programming, 2nd Ed., Addison-Wesley, Reading, MA,
1984
P.E.Gill,W.MurrayandM.H.Wright,PracticalOptimization,AcademicPress,NewYork,1981
J.Nocedal,UpdatingQuasi-NewtonMatriceswithLimitedStorage,Math.Comp.,773-782(1980)
S. J. Watowich, E. S. Meyer, R. Hagstrom and R. Josephs, A Stable, Rapidly Converging Conjugate
GradientMethodforEnergyMinimization,J.Comput.Chem.,9,650-661(1988)
W.C.Davidon,OptimallyConditionedOptimizationAlgorithmswithoutLineSearches,Math.Prog.,9,
1-30(1975)
TRUNCATEDNEWTONOPTIMIZATION
J. W. Ponder and F. M. Richards, An Efficient Newton-like Method for Molecular Mechanics Energy
MinimizationofLargeMolecules,J.Comput.Chem.,8,1016-1024(1987)
R. S. Dembo and T. Steihaug, Truncated-Newton Algorithms for Large-Scale Unconstrained
Optimization,Math.Prog.,26,190-212(1983)
S.C.EisenstatandH.F.Walker,ChoosingtheForcingTermsinanInexactNewtonMethod,SIAMJ.
Sci.Comput.,17,16-32(1996)
T.SchlickandM.Overton,APowerfulTruncatedNewtonMethodforPotentialEnergyMinimization,
J.Comput.Chem.,8,1025-1039(1987)
D. S. Kershaw, The Incomplete Cholesky-Conjugate Gradient Method for the Iterative Solution of
SystemsofLinearEquations,J.Comput.Phys.,26,43-65(1978)
208
TINKERUser'sGuide
208
T.A.Manteuffel,AnIncompleteFactorizationTechniqueforPositiveDefiniteLinearSystems,Math.
Comp.,34,473-497(1980)
P.Derreumaux,G.ZhangandT.SchlickandB.R.Brooks,ATruncatedNewtonMinimizerAdaptedfor
CHARMMandBiomolecularApplications,J.Comput.Chem.,15,532-552(1994)
I.S.Duff,A.M.ErismanandJ.K.Reid,DirectMethodsforSparseMatrices,OxfordUniversityPress,
Oxford,1986
POTENTIALENERGYSMOOTHING
R. V. Pappu, R. K. Hart and J. W. Ponder, Analysis and Application of Potential Energy Smoothing
MethodsforGlobalOptimization,J.Phys.Chem.B,102,9725-9742(1998)
L. Piela, J. Kostrowicki and H. A. Scheraga, The Multiple-Minima Problem in the Conformational
Analysis of Molecules. Deformation of the Potential Energy Hypersurface by the Diffusion Equation
Method,J.Phys.Chem.,93,3339-3346(1989)
J. Ma and J. E. Straub, Simulated Annealing Using the Classical Density Distribution, J. Chem. Phys.,
101,533-541(1994)
C.TsooandC.L.Brooks,ClusterStructureDeterminationUsingGaussianDensityDistributionGlobal
MinimizationMethods,J.Chem.Phys.,101,6405-6411(1994)
S. Nakamura, H. Hirose, M. Ikeguchi and J. Doi, Conformational Energy Minimization Using a TwoStageMethod,J.Phys.Chem.,99,8374-8378(1995)
T. Huber, A. E. Torda and W. F. van Gunsteren, Structure Optimization Combining Soft-Core
InteractionFunctions,theDiffusionEquationMethod,andMolecularDynamics,J.Phys.Chem.A,101,
5926-5930(1997)
S. Schelstraete and H. Verschelde, Finding Minimum-Energy Configurations of Lennard-Jones
ClustersUsinganEffectivePotential,J.Phys.Chem.A,101,310-315(1998)
I.AndricioaeiandJ.E.Straub,GlobalOptimizationUsingBadDerivatives:Derivative-FreeMethodfor
MolecularEnergyMinimization,J.Comput.Chem.,19,1445-1455(1998)
L. Piela, Search for the Most Stable Structures on Potential Energy Surfaces, Coll. Czech. Chem.
Commun.,63,1368-1380(1998)
``SNIFFER''GLOBALOPTIMIZATION
A.O.Griewank,GeneralizedDescentforGlobalOptimization,J.Opt.Theor.Appl.,34,11-39(1981)
R.A.R.ButlerandE.E.Slaminka,AnEvaluationoftheSnifferGlobalOptimizationAlgorithmUsing
StandardTestFunctions,J.Comput.Phys.,99,28-32(1993)
J. W. Rogers and R. A. Donnelly, Potential Transformation Methods for Large-Scale Global
Optimization,SIAMJ.Optim.,5,871-891(1995)
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INTEGRATIONMETHODSFORMOLECULARDYNAMICS
D. Beeman, Some Multistep Methods for Use in Molecular Dynamics Calculations, J. Comput. Phys.,
20,130-139(1976)
M.LevittandH.Meirovitch,IntegratingtheEquationsofMotion,J.Mol.Biol.,168,617-620(1983)
J. Aqvist, W. F. van Gunsteren, M. Leijonmarck and O. Tapia, A Molecular Dynamics Study of the CTerminalFragmentoftheL7/L12RibosomalProtein,J.Mol.Biol.,183,461-477(1985)
W. C. Swope, H. C. Andersen, P. H. Berens and K. R. Wilson, A Computer Simulation Method for the
CalculationofEquilibriumConstantsfortheFormationofPhysicalClustersofMolecules:Application
toSmallWaterClusters,J.Chem.Phys.,76,637-649(1982)
CONSTRAINTDYNAMICS
W.F.vanGunsterenandH.J.C.Berendsen,AlgorithmsforMacromolecularDynamicsandConstraint
Dynamics,Mol.Phys.,34,1311-1327(1977)
G. Ciccotti, M. Ferrario and J.-P. Ryckaert, Molecular Dynamics of Rigid Systems in Cartesian
Coordinates:AGeneralFormulation,Mol.Phys.,47,1253-1264(1982)
H. C. Andersen, Rattle: A ``Velocity'' Version of the Shake Algorithm for Molecular Dynamics
Calculations,J.Comput.Phys.,52,24-34(1983)
R.Kutteh,RATTLERecipeforGeneralHolonomicConstraints:AngleandTorsionConstraints,CCP5
Newsletter,
46,
9-17
(1998)
[available
from
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web
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at
http://www.dl.ac.uk/CCP/CCP5/newsletter_index.html]
B.J.Palmer,DirectApplicationofSHAKEtotheVelocityVerletAlgorithm,J.Comput.Phys.,104,470472(1993)
S.MiyamotoandP.A.Kollman,SETTLE:AnAnalyticalVersionoftheSHAKEandRATTLEAlgorithm
forRigidWaterModels,J.Comput.Chem.,13,952-962(1992)
B. Hess, H. Bekker, H. J. C. Berendsen and J. G. E. M. Fraaije, LINCS: A Linear Constraint Solver for
MolecularSimulations,J.Comput.Chem.,18,1463-1472(1997)
J. T. Slusher and P. T. Cummings, Non-Iterative Constraint Dynamics using Velocity-Explicit Verlet
Methods,Mol.Simul.,18,213-224(1996)
LANGEVIN,BROWNIANANDSTOCHASTICDYNAMICS
M.P.Allen,BrownianDynamicsSimulationofaChemicalReactioninSolution,Mol.Phys.,40,10731087(1980)
W.F.vanGunsterenandH.J.C.Berendsen,AlgorithmsforBrownianDynamics,Mol.Phys.,45,637647(1982)
210
TINKERUser'sGuide
210
F.GuarnieriandW.C.Still,ARapidlyConvergentSimulationMethod:MixedMonteCarlo/Stochastic
Dynamics,J.Comput.Chem.,15,1302-1310(1994)
M.G.PaterliniandD.M.Ferguson,ConstantTemperatureSimulationsusingtheLangevinEquation
withVelocityVerletIntegration,Chem.Phys.,236,243-252(1998)
CONSTANTTEMPERATUREANDPRESSUREDYNAMICS
H.J.C.Berendsen,J.P.M.Postma,W.F.vanGunsteren,A.DiNolaandJ.R.Haak,MolecularDynamics
withCouplingtoanExternalBath,J.Chem.Phys.,81,3684-3690(1984)
W. G. Hoover, Canonical Dynamics: Equilibrium Phase-space Distributions, Phys. Rev. A, 31, 16951697(1985)
J. J. Morales, S. Toxvaerd and L. F. Rull, Computer Simulation of a Phase Transition at Constant
TemperatureandPressure,Phys.Rev.A,34,1495-1498(1986)
B. R. Brooks, Algorithms for Molecular Dynamics at Constant Temperature and Pressure, Internal
ReportofDivisionofComputerResearchandTechnology,NationalInstitutesofHealth,1988.
M. Levitt, Molecular Dynamics of Native Protein: Computer Simulation of Trajectories, J. Mol. Biol.,
168,595-620(1983)
OUT-OF-PLANEDEFORMATIONTERMS
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