VMD-L Mailing List

From: Qinghua Liao (scorpio.liao_at_gmail.com)
Date: Wed Jun 21 2017 - 16:58:52 CDT

Hello,

Continue on this topic, I found that the charge group in the converted
Gromacs topology file is totally messed up.
Some charge groups contain several residues, I guess that charge groups
are not defined in the psf file. How could this happen? Could some one
give a clue? Thanks a lot!

All the best,
Qinghua

On 06/21/2017 08:04 PM, Axel Kohlmeyer wrote:
> On Wed, Jun 21, 2017 at 1:20 PM, Qinghua Liao <scorpio.liao_at_gmail.com>
> 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!
>>
> ​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
>
> https://sites.google.com/site/akohlmey/software/topotools
>
> ​please let us know, if the ​problem persists.
>
> thanks,
> ​ ​
> ​axel.​
>
>
>
>>
>> All the best,
>> Qinghua
>>
>
>