vmd教程 forces-tutorial

1TCLFORCES13

1.4Example3:ForcingaSubsetofAtoms

Thisexampledealswiththeimportantabilitytoforceasubsetofyouratoms.Inthissection,wewillapplyforcesonlytothebackboneatomsoftheprotein.Weaccomplishthisbymakingaspecial“targetatom”PDB le,usingthebetacolumntomarktheatomswewanttoapplyforceto.Inaddition,wewillusetheoccupancycolumntotellourscripttheatomicmasses,inordertodemon-stratehowtoprovidethescriptwithadditionalinformation.

1Changetothedirectoryforces-tutorial-files/tclForcesFiles/rot-b.2Asusual,wewill rstexaminetheNAMDcon guration le.Openthe lerot-b-short.namd.First,notethatwearenowusingadi erentsystem,oneinwhichtheubiquitinhasbeensolvated.Thisisamorenaturalenvironmentfortheprotein.

Lookattheendofthe le,wherewesetuptclForces.Weseeanewline:

settargetAtomPdb../common/ubiquitinbackbone.pdb

Withthisline,wespecifytheaforementionedtargetatomPDB le.Thus,our rsttaskistoproducethat le.WewilluseaVMDscripttoaccom-plishthis.

3Openthe lemakeTargetAtomPdb.tcl.The rstsectionsetsafewvari-ables.First,therelevant lenames:

setpdbcommon/ubiquitinsetpsfcommon/ubiquitinsettargetPdbcommon/ubiquitinNext,wesettheselectiontextwewillusetoselectouratoms,andthebetavaluethattheseatomswillreceive:

setselection"proteinandbackbone"

settargetMark"1.00"

4Next,weloadthestructureintoVMD,andsetboththebetaandoccu-pancycolumnstozero:

molloadpsf$psfpdb$pdb

setall[atomselecttopall]

$allsetbeta0

$allsetoccupancy0

5Nowwemakeaselectionofthetargetatoms,settheirbetaandoccupancycolumnstotheappropriatevalues,andwritetheoutputPDB.Notetheeasewithwhichthelistofmassesareusedtosettheoccupancy: