From: Vermaas, Joshua (
Date: Wed Jun 21 2017 - 13:30:42 CDT

Hi Qinghua,

This was a bug introduced shortly before the release of VMD 1.9.3, and involves a [...] hidden in text. This gets interpreted by Tcl as a command, and since there is no "..." command, causes a definite problem. The fix involved is pretty simple, but does involve changing a file by hand. See


On 06/21/2017 12:25 PM, Qinghua Liao wrote:

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!

All the best,