VMD-L Mailing List

From: Radak, Brian K (bradak_at_anl.gov)
Date: Wed Jun 21 2017 - 17:03:23 CDT

Charge groups are definitely not defined in the PSF format. Are these used for anything anymore?


Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory

9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643
brian.radak_at_anl.gov
________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Qinghua Liao <scorpio.liao_at_gmail.com>
Sent: Wednesday, June 21, 2017 4:58:52 PM
To: Vmd l
Subject: Re: vmd-l: convert psf to top with topotools

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
>>
>
>