From: Axel Kohlmeyer (
Date: Wed Jun 21 2017 - 13:04:40 CDT

On Wed, Jun 21, 2017 at 1:20 PM, Qinghua Liao <>

> Hello,
> I have used psfgen in vmd to generate the psf file of my protein, then I
> want to convert the psf file to top file with topotools,
> but I failed.
> I used these commands:
> package require topotools
> mol load psf ubq.psf pdb ubq.pdb
> topo writegmxtop [list ../../common/par_all27_prot_lipid.inp]
> then I got the error of " *invalid command name "..." *"
> But if I remove [list ../../common/par_all27_prot_lipid.inp ], then I can
> get the gmx top file, but it does not have all the parameters
> for the topology file. Could someone give me some tips? Thanks a lot!

​please upgrade to the latest version of the topotools plugin. yours seems
to have a bug that has already been fixed.

in between VMD releases, you can find updated topotools versions with
bugfixes at the URL below.
the latest update was on april 13th, 2017

​please let us know, if the ​problem persists.

​ ​

> All the best,
> Qinghua

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