From: Florentina Tofoleanu (
Date: Wed May 20 2009 - 11:34:18 CDT

I'm using this script to calculate it, but I'm getting the same value for
each of the frames:

mol load pdb X.pdb
mol load psf X.psf
mol load dcd X.dcd

set outfile [open com.dat w];

set numframes [molinfo top get numframes];

set refA [atomselect 0 "chain A and not hydrogen"]
set refB [atomselect 0 "chain B and not hydrogen"]

for {set frame 0} {$frame < $numframes} {incr frame} {
$refA frame $frame
$refB frame $frame
$refA update
$refB update
set com1 [measure center $refA weight mass]
set com2 [measure center $refB weight mass]
lappend simdata [veclength [vecsub $com1 $com2]]
puts $outfile “$simdata”;
close $outfile

I've read the messages posted before related to this issue, but can't really
find the problem with this script. Could someone please show me what's wrong
with it and help me correcting it?


Florentina Tofoleanu
Postgraduate Research Fellow
Theoretical and Computational Biophysics Group
University College Dublin
School of Physics, Rm. 110
Belfield, Dublin 4, Ireland