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1、GROMACSTutorialLysozymeinWaterJustinLemkulDepartmentofBiochemistry,VirginiaTechThisexamplewillguideanewuserthroughtheprocessofsettingupasimulationsystemcontainingaprotein(lysozyme)inaboxofwater,withions.Eachstepwillcontainanexplanationofinputandoutput,usingtypicalsettingsforgeneraluse.Thistu
2、torialassumesyouareusingaGROMACSversioninthe4.5.xseries.GROMACSTutorialStepOne:PreparetheTopologyWemustdownloadtheproteinstructurefilewewillbeworkingwith.Forthistutorial,wewillutilizeheneggwhitelysozyme(PDBcode1AKI).GototheRCSBwebsiteanddownloadthePDBtextforthecrystalstructure.Onceyouhavedow
3、nloadedthestructure,youcanvisualizethestructureusingaviewingprogramsuchasVMD,Chimera,PyMOL,etc.Onceyou'vehadalookatthemolecule,youaregoingtowanttostripoutthecrystalwaters.Useaplaintexteditorlikevi,emacs(Linux/Mac),orNotepad(Windows).Donotusewordprocessingsoftware!Deletethelinescorrespondingt
4、othesemolecules(residue"HOH"inthePDBfile).Notethatsuchaprocedureisnotuniversallyappropriate(i.e.,thecaseofaboundactivesitewatermolecule).Forourintentionshere,wedonotneedcrystalwater.Alwayscheckyour.pdbfileforentrieslistedunderthecommentMISSING,astheseentriesindicateeitheratomsorwholeresidues
5、thatarenotpresentinthecrystalstructure.Terminalregionsmaybeabsent,andmaynotpresentaproblemfordynamics.Incompleteinternalsequencesoranyaminoacidresiduesthathavemissingatomswillcausepdb2gmxtofail.Thesemissingatoms/residuesmustbemodeledinusingothersoftwarepackages.Alsonotethatpdb2gmxisnotmagic.
6、Itcannotgeneratetopologiesforarbitrarymolecules,justtheresiduesdefinedbytheforcefield(inthe*.rtpfiles-generallyproteins,nucleicacids,andaveryfiniteamountofcofactors,likeNAD(H)andATP).Nowthatthecrystalwatersaregoneandwehaveverifiedthatallthenecessaryatomsarepresent,thePDBfileshouldcontainonly
7、proteinatoms,andisreadytobeinputintothefirstGROMACStool,pdb2gmx.Thepurposeofpdb2gmxistogeneratethreefiles:1.Thetopologyforthemolecule.2.Apositionrestraintfile.3.Apost-processedstructurefile.Thetopology(topol.topbydefault)containsalltheinformationne
