From: Axel Kohlmeyer (
Date: Sun Oct 18 2015 - 09:39:43 CDT

this is a VMD question and not a NAMD question, so i am redirecting it to
the VMD mailing list (where it belongs).

On Sun, Oct 18, 2015 at 8:52 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?

while the error message is comping from the mergemols command, ‚Äčthe error
message hints‚Äč at some error in loading molecules/files during the
construction of your midlist variable.

i just made a simple test and have no difficulties merging 180 or more


> 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.