VMD-L Mailing List

From: Qinghua Liao (scorpio.liao_at_gmail.com)
Date: Wed Jun 21 2017 - 13:35:12 CDT

Dear Axel and Joshua,

Thanks very much for both of your reply. After upgrading to the newest
version of topotools, I can
do the conversion successfully! Thanks a lot!

All the best,
Qinghua

On 06/21/2017 08:30 PM, Vermaas, Joshua wrote:
> 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 http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/28195.html.
>
> -Josh
>
> On 06/21/2017 12:25 PM, Qinghua Liao wrote:
> 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 ubq.top [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,
> Qinghua
>