From: Joaquim Rui de Castro Rodrigues (
Date: Tue Oct 20 2015 - 07:24:14 CDT

Dear Liu Wei,

You have an unmatched ] in your lappend lines.

Rui Rodrigues

De: [] Em Nome De Axel Kohlmeyer []
Enviado: terça-feira, 20 de Outubro de 2015 11:58
Para: wliu
Cc: VMD Mailing List
Assunto: Re: vmd-l: Problem on merging multi-psf files into one

i already answered your question. the problem has to be in how you load the molecules and build midlist, not with TopoTools::mergemols.


On Tue, Oct 20, 2015 at 1:47 AM, wliu <<>> wrote:
Dear all,

I have 180 PSF and 180 PDB files which has same chain name but different coordinates. I need to merge these 180 PSF files into one. And I write a tcl script as

package require topotools 1.0
set midlist {}
 set mol [mol new 1tcl.psf waitfor all]
 mol addfile 1tcl.pdb
 lappend midlist $mol]
 set mol [mol new 180tcl.psf waitfor all]
 mol addfile 180tcl.pdb
 lappend midlist $mol]
set mol [::TopoTools::mergemols $midlist]
animate write psf merge.psf $mol
animate write pdb merge.pdb $mol

But when I run this script with VMD, I saw an error as

Main< (TclPsfGen) 37 % source MergePSF.tcl
-error molecule id 1] does not exist.

Then I checked and I found when VMD run the command 'set mol [::TopoTools::mergemols $midlist]', it turns out to have this error. So my question is, why I got this error? How to fix it and get a right merged psf file?

I would very much appreciate for the helps!
Liu Wei

Dr. Axel Kohlmeyer<>
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.