VMD-L Mailing List

From: wliu (wliu_at_itcs.ecnu.edu.cn)
Date: Tue Oct 20 2015 - 00:47:12 CDT

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