From: Salvatore Mario Cosseddu (
Date: Wed May 18 2011 - 10:10:22 CDT

the script is not full... in this form it could not work. you at least

need a "}" at the end of the for loop and setting some variables...

what do you means by loops thorough it? something like

for i in {1..3};
vmd -dispdev text -e tet.vmd ;
vmd -dispdev text -e tet2.vmd ;
echo $i;

because it should work if there's no bus in the tcl script and it finish
with exit. May you post the full script?

On 18/05/11 13:04, Jorgen Simonsen wrote:
> Hi all
> I have organized my output in different directories and would like to
> use some packages within vmd to analyse the output - I have naively
> put my script together like this,mrun
> #!/bin/bash
> vmd -dispdev text new_myfile.psf new_model.pdb -e tet.scr
> vmd -dispdev text new_myfile.psf new_model.pdb -e tet2.scr
> vmd -dispdev text new_myfile.psf new_model.pdb -e tet3.scr
> the tet.scr contain the following
> for { set i 1 } { $i $\leq$ $nf } { incr i } {
> $sel frame $i
> $sel move [measure fit $sel $frame0]
> puts $outfile "[measure rmsd $sel $frame0]"
> quit
> where 2 and 3 are modifications. If I do manually go to a directory and
> source
> it works fine but if I loop thorugh it - it opens and immediately
> quits the application.
> Thanks,

Salvatore Cosseddu
PhD student
Centre for Scientific Computing and School of Engineering
University of Warwick
Coventry CV4 7AL
United Kingdom