vmd教程 forces-tutorial(14)

vmd教程 forces-tutorial

1TCLFORCES

settarget[atomselecttop$selection]

setmasses[$targetgetmass]

$targetsetbeta$targetMark

$targetsetoccupancy$masses

$allwritepdb$targetPdb

exit

6Nowrunthescript:

vmd-dispdevtext-emakeTargetAtomPdb.tcl14

(Note:ForWindowsusers,opentheVMDGUIandsourcethescript leintheTkConsole.)

Ifyouwereunabletorunthescript,copythe leexample-output/ubiquitinsolvateintothecommondirectory.

7Next,takealookatthetclForcesscript.Openthe lerot-b.tcl.Rightfromthebeginning,wenoticemanydi erences.It rstsetsatargetMarkvariablesothatthescriptcanrecognizethemarkswe’vesetinthetargetPDB:

settargetMark1.0

8NowwehavetoprocessthePDB.Therearenobuilt-inroutinesforac-complishingthis,sothefollowingcodeisquitelow-level.ThecolumnsofaPDB lehavea xedcharacterwidth,sowemustsimplyreadeachline,andbreakitinto xed-sizedpiecesaccordingtothePDBformat:

settargets{}

setmasses{}

setinStream[open$targetAtomPdbr]

foreachline[split[read$inStream]\n]{

settype[stringtrim[stringrange$line05]]

setname[stringtrim[stringrange$line1215]]

setresid[stringtrim[stringrange$line2225]]

setbeta[stringtrim[stringrange$line6065]]

setoccupancy[stringtrim[stringrange$line5459]]

setsegname[stringtrim[stringrange$line7275]]

9We rstmakesurethatthislinecorrespondstoanatomrecordandnotacommentlineorsomeotherentry.Then,iftheatomhasabetavaluematchingthetargetvalue,weformatripleconsistingoftheatom’ssegname,resid,andname.Thisisnecessaryfor ndingtheindexoftheatom: