From: bora erdemli (boraerdemli_at_yahoo.com)
Date: Fri Sep 03 2004 - 00:23:42 CDT
Hi,
I am using the folowing rmsd.tcl with the VMD for
Win32,version 1.8.2...
set outfile [open rmsd.dat w]
set nf [molinfo top get numframes]
set frame0 [atomselect top "selection" frame 0]
#or h]
# rmsd calculation loop
for { set i 1 } { $i <= $nf } { incr i } {
set sel [atomselect top "selection" frame $i]
$sel move [measure fit $sel $frame0]
puts $outfile "[measure rmsd $sel $frame0]"
}
close $outfile
--- John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> Which rmsd.tcl script are you using, and with
> which version of VMD?
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Aug 26, 2004 at 12:10:05PM -0700, bora
> erdemli wrote:
> >
> > Hi,
> > I use the rmsd.tcl script which is in the VMD
> website.
> > ýt works well for the whole protein but when I try
> to
> > calculate the rmsd of a residue or sidechain of it
> it
> > gave me unexpectedly small rmsd .
> > Is there anybody who has an idea that what the
> reason
> > of it and have any sugestion ?
> > thanks in advance....
> >
> > Bora
> > Koc University
> > Computational Science and Engineering
> > Istanbul,Turkey
> >
> >
> >
> > __________________________________
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> --
> NIH Resource for Macromolecular Modeling and
> Bioinformatics
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> Technology
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>
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