VMD-L Mailing List

From: Qinghua Liao (scorpio.liao_at_gmail.com)
Date: Wed Jun 21 2017 - 17:45:11 CDT

Hello Brian,

Thanks very much for your reply! Here is the beginning of the converted
topology in Gromacs format:
#
; nr type resnr residue atom cgnr charge mass
      1 N287 1 MET N 1 -0.3000 14.0067
      2 H290 1 MET HT1 1 0.3300 1.0079
      3 H290 1 MET HT2 1 0.3300 1.0079
      4 H290 1 MET HT3 1 0.3300 1.0079
      5 C293 1 MET CA 1 0.2500 12.0107
      6 H140 1 MET HA 2 0.0600 1.0079
      7 C136 1 MET CB 2 -0.1200 12.0107
      8 H140 1 MET HB1 2 0.0600 1.0079
      9 H140 1 MET HB2 3 0.0600 1.0079
     10 C210 1 MET CG 3 0.0475 12.0107
     11 H140 1 MET HG1 3 0.0600 1.0079
     12 H140 1 MET HG2 3 0.0600 1.0079
     13 S202 1 MET SD 3 -0.3350 32.0650
     14 C209 1 MET CE 3 -0.0125 12.0107
     15 H140 1 MET HE1 3 0.0600 1.0079
     16 H140 1 MET HE2 3 0.0600 1.0079
     17 H140 1 MET HE3 4 0.0600 1.0079
     18 C235 1 MET C 4 0.5000 12.0107
     19 O236 1 MET O 5 -0.5000 15.9994
     20 N238 2 PHE N 5 -0.5000 14.0067
     21 H241 2 PHE HN 5 0.3000 1.0079
     22 C224 2 PHE CA 5 0.1400 12.0107
#

As you can see, the charge groups converted by topotools are totally
messed up. HB2 is defined in charge group 3, but not 2 with CB,
and group 5 contains atoms from both MET and PHE.

All the best,
Qinghua

On 06/22/2017 12:03 AM, Radak, Brian K wrote:
> 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
>>>
>>