一个使用gromacs进行蛋白质模拟的入门教程Word下载.docx
- 文档编号:15225759
- 上传时间:2022-10-28
- 格式:DOCX
- 页数:17
- 大小:976.43KB
一个使用gromacs进行蛋白质模拟的入门教程Word下载.docx
《一个使用gromacs进行蛋白质模拟的入门教程Word下载.docx》由会员分享,可在线阅读,更多相关《一个使用gromacs进行蛋白质模拟的入门教程Word下载.docx(17页珍藏版)》请在冰豆网上搜索。
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.,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.
Thetopologybydefault)containsalltheinformationnecessarytodefinethemoleculewithinasimulation.Thisinformationincludesnonbondedparameters(atomtypesandcharges)aswellasbondedparameters(bonds,angles,anddihedrals).Wewilltakeamoredetailedlookatthetopologyonceithasbeengenerated.
Executepdb2gmxbyissuingthefollowingcommand:
pdb2gmx-f-o-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)-version
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:
,and.isaGROMACS-formattedstr
- 配套讲稿:
如PPT文件的首页显示word图标,表示该PPT已包含配套word讲稿。双击word图标可打开word文档。
- 特殊限制:
部分文档作品中含有的国旗、国徽等图片,仅作为作品整体效果示例展示,禁止商用。设计者仅对作品中独创性部分享有著作权。
- 关 键 词:
- 一个 使用 gromacs 进行 蛋白质 模拟 入门教程