一个使用gromacs进行蛋白质模拟的入门教程.docx

一个使用gromacs进行蛋白质模拟的入门教程.docx

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一个使用gromacs进行蛋白质模拟的入门教程

GROMACSTutorial

LysozymeinWater

JustinLemkul

DepartmentofBiochemistry,VirginiaTech

Thisexamplewillguideanewuserthroughtheprocessofsettingupasimulationsystemcontainingaprotein（lysozyme）inaboxofwater,withions.Eachstepwillcontainanexplanationofinputandoutput,usingtypicalsettingsforgeneraluse.

ThistutorialassumesyouareusingaGROMACSversioninthe4.5.xseries.

GROMACSTutorial

StepOne:

PreparetheTopology

Wemustdownloadtheproteinstructurefilewewillbeworkingwith.Forthistutorial,wewillutilizeheneggwhitelysozyme（PDBcode1AKI）.GototheRCSBwebsiteanddownloadthePDBtextforthecrystalstructure.

Onceyouhavedownloadedthestructure,youcanvisualizethestructureusingaviewingprogramsuchasVMD,Chimera,PyMOL,etc.Onceyou'vehadalookatthemolecule,youaregoingtowanttostripoutthecrystalwaters.Useaplaintexteditorlikevi,emacs（Linux/Mac）,orNotepad（Windows）.Donotusewordprocessingsoftware!

Deletethelinescorrespondingtothesemolecules（residue"HOH"inthePDBfile）.Notethatsuchaprocedureisnotuniversallyappropriate（i.e.,thecaseofaboundactivesitewatermolecule）.Forourintentionshere,wedonotneedcrystalwater.

Alwayscheckyour.pdbfileforentrieslistedunderthecommentMISSING,astheseentriesindicateeitheratomsorwholeresiduesthatarenotpresentinthecrystalstructure.Terminalregionsmaybeabsent,andmaynotpresentaproblemfordynamics.Incompleteinternalsequencesoranyaminoacidresiduesthathavemissingatomswillcausepdb2gmxtofail.Thesemissingatoms/residuesmustbemodeledinusingothersoftwarepackages.Alsonotethatpdb2gmxisnotmagic.Itcannotgeneratetopologiesforarbitrarymolecules,justtheresiduesdefinedbytheforcefield（inthe*.rtpfiles-generallyproteins,nucleicacids,andaveryfiniteamountofcofactors,likeNAD（H）andATP）.

Nowthatthecrystalwatersaregoneandwehaveverifiedthatallthenecessaryatomsarepresent,thePDBfileshouldcontainonlyproteinatoms,andisreadytobeinputintothefirstGROMACStool,pdb2gmx.Thepurposeofpdb2gmxistogeneratethreefiles:

1.Thetopologyforthemolecule.

2.Apositionrestraintfile.

3.Apost-processedstructurefile.

Thetopology（topol.topbydefault）containsalltheinformationnecessarytodefinethemoleculewithinasimulation.Thisinformationincludesnonbondedparameters（atomtypesandcharges）aswellasbondedparameters（bonds,angles,anddihedrals）.Wewilltakeamoredetailedlookatthetopologyonceithasbeengenerated.

Executepdb2gmxbyissuingthefollowingcommand:

pdb2gmx-f1AKI.pdb-o1AKI_processed.gro-waterspce

Thestructurewillbeprocessedbypdb2gmx,andyouwillbepromptedtochooseaforcefield:

SelecttheForceField:

From'/usr/local/gromacs/share/gromacs/top':

1:

AMBER03forcefield（Duanetal.,J.Comp.Chem.24,1999-2012,2003）

2:

AMBER94forcefield（Cornelletal.,JACS117,5179-5197,1995）

3:

AMBER96forcefield（Kollmanetal.,Acc.Chem.Res.29,461-469,1996）

4:

AMBER99forcefield（Wangetal.,J.Comp.Chem.21,1049-1074,2000）

5:

AMBER99SBforcefield（Hornaketal.,Proteins65,712-725,2006）

6:

AMBER99SB-ILDNforcefield（Lindorff-Larsenetal.,Proteins78,1950-58,2010）

7:

AMBERGSforcefield（Garcia&Sanbonmatsu,PNAS99,2782-2787,2002）

8:

CHARMM27all-atomforcefield（withCMAP）-version2.0

9:

GROMOS9643a1forcefield

10:

GROMOS9643a2forcefield（improvedalkanedihedrals）

11:

GROMOS9645a3forcefield（SchulerJCC2001221205）

12:

GROMOS9653a5forcefield（JCC2004vol25pag1656）

13:

GROMOS9653a6forcefield（JCC2004vol25pag1656）

14:

OPLS-AA/Lall-atomforcefield（2001aminoaciddihedrals）

15:

[DEPRECATED]Encadall-atomforcefield,usingfullsolventcharges

16:

[DEPRECATED]Encadall-atomforcefield,usingscaled-downvacuumcharges

17:

[DEPRECATED]Gromacsforcefield（seemanual）

18:

[DEPRECATED]GromacsforcefieldwithhydrogensforNMR

Theforcefieldwillcontaintheinformationthatwillbewrittentothetopology.Thisisaveryimportantchoice!

Youshouldalwaysreadthoroughlyabouteachforcefieldanddecidewhichismostapplicabletoyoursituation.Forthistutorial,wewillusetheall-atomOPLSforcefield,sotype14atthecommandprompt,followedby'Enter'.

Therearemanyotheroptionsthatcanbepassedtopdb2gmx.Somearelistedhere:

-ignh:

IgnoreHatomsinthePDBfile;especiallyusefulforNMRstructures.Otherwise,ifHatomsarepresent,theymustbeinthecorrectorderandnamedexactlyhowGROMACSexpectsthemtobe.

-ter:

InteractivelyassignchargestatesforN-andC-termini.

-inter:

InteractivelyassignchargestatesforGlu,Asp,Lys,Arg,andHis;assigndisulfidestoCys.

Youhavenowgeneratedthreenewfiles:

1AKI_processed.gro,topol.top,andposre.itp.1AKI_processed.groisaGROMACS-formattedstructurefilethatcontainsalltheatomsdefinedwithintheforcefield（i.e.,Hatomshavebeenaddedtotheaminoacidsintheprotein）.Thetopol.topfileisthesystemtopology（moreonthisinaminute）.Theposre

.itpfilecontainsinformationusedtorestrainthepositionsofheavyatoms（moreonthislater）.

StepTwo:

ExaminetheTopology

Let'slookatwhatisintheoutputtopology（topol.top）.Again,usingaplaintexteditor,inspectitscontents.Afterseveralcommentlines（precededby;）,youwillfindthefollowing:

#include"oplsaa.ff/forcefield.itp"

ThislinecallstheparameterswithintheOPLS-AAforcefield.Itisatthebeginningofthefile,indicatingthatallsubsequentparametersarederivedfromthisforcefield.Thenextimportantlineis [moleculetype],belowwhichyouwillfind

;Namenrexcl

Protein_A3

Thename"Protein_A"definesthemoleculename,basedonthefactthattheproteinwaslabeledaschainAinthePDBfile.Thereare3exclusionsforbondedneighbors.MoreinformationonexclusionscanbefoundintheGROMACSmanual;adiscussionofthisinformationisbeyondthescopeofthistutorial.

Thenextsectiondefinesthe [atoms] intheprotein.Theinformationispresentedascolumns:

[atoms]

;nrtyperesnrresidueatomcgnrchargemasstypeBchargeBmassB

;residue1LYSrtpLYSHq+2.0

1opls_2871LYSN1-0.314.0067;qtot-0.3

2opls_2901LYSH110.331.008;qtot0.03

3opls_2901LYSH210.331.008;qtot0.36

4opls_2901LYSH310.331.008;qtot0.69

5opls_293B1LYSCA10.2512.011;qtot0.94

6opls_1401LYSHA10.061.008;qtot1

Theinterpretationofthisinformationisasfollows:

∙nr:

Atomnumber

∙type:

Atomtype

∙resnr:

Aminoacidresiduenumber

∙residue:

Theaminoacidresiduename

Notethatthisresiduewas"LYS"inthePDBfile;theuseof.rtpentry"LYSH"indicatesthattheresidueisprotonated（thepredominantstateatneutralpH）.

∙atom:

Atomname

∙cgnr:

Chargegroupnumber

Chargegroupsdefineunitsofintegercharge;theyaidinspeedingupcalculations

∙charge:

Self-explanatory

The"qtot"descriptorkeepsarunningcountofthetotalchargeonthemolecule

∙mass:

Alsoself-explanatory

∙typeB,chargeB,massB:

Usedforfreeenergyperturbation（notdiscussedhere）

Subsequentsectionsinclude [bonds],[pairs],[angles], and [dihedrals].Someofthesesectionsareself-explanatory（bonds,angles,anddihedrals）.TheparametersandfunctiontypesassociatedwiththesesectionsareelaboratedoninChapter5oftheGROMACSmanual.Special1-4interactionsareincludedunder"pairs"（section5.3.4oftheGROMACSmanual）.

Theremainderofthefileinvolvesdefiningafewotheruseful/necessarytopologies,startingwithpositionrestraints.The"posre.itp"filewasgeneratedbypdb2gmx;itdefinesaforceconstantusedtokeepatomsinplaceduringequilibration（moreonthislater）.

;IncludePositionrestraintfile

#ifdefPOSRES

#include"posre.itp"

#endif

Thisendsthe"Protein_A"moleculetypedefinition.Theremainderofthetopologyfileisdedicatedtodefiningothermoleculesandprovidingsystem-leveldescriptions.Thenextmoleculetype（bydefault）isthesolvent,inthiscaseSPC/Ewater.OthertypicalchoicesforwaterincludeSPC,TIP3P,andTIP4P.Wechosethisbypassing"

-waterspce"topdb2gmx.Foranexcellentsummaryofthemanydifferentwatermodels,click here,butbeawarethatnotallofthesemodelsarepresentwithinGROMACS.

;Includewatertopology

#include"oplsaa.ff/spce.itp"

#ifdefPOSRES_WATER

;Positionrestraintforeachwateroxygen

[position_restraints]

;ifunctfcxfcyfcz

11100010001000

#endif

Asyoucansee,watercanalsobeposition-restrained,usingaforceconstant（kpr）of1000kJmol-1 nm-2.

Ionparametersareincludednext:

;Includegenerictopologyforions

#include"oplsaa.ff/ions.itp"

Finallycomesystem-leveldefinitions.The [system] directivegivesthenameofthesystemthatwillbewrittentooutputfilesduringthesimulation.The [molecules] directivelistsallofthemoleculesinthesystem.

[system]

;Name

LYSOZYME

[molecules]

;Compound#mols

Protein_A1

Afewkeynotesaboutthe [molecules] directive:

1.Theorderofthelistedmoleculesmust exactly matchtheorderofthemoleculesinthecoordinate（inthiscase,.gro）file.

2.Thenameslistedmustmatchthe [moleculetype] nameforeachspecies,notresiduenamesoranythingelse.

Ifyoufailtosatisfytheseconcreterequirementsatanytime,youwillgetfatalerrorsfromgrompp（discussedlater）aboutmismatchednames,moleculesnotbeingfound,oranumberofothers.

Nowthatwehaveexaminedthecontentsofatopologyfile,wecancontinuebuildingoursystem.

StepThree:

DefiningtheUnitCell&AddingSolvent

Nowthatyouarefamiliar