VMD-L Mailing List

From: Qinghua Liao (scorpio.liao_at_gmail.com)
Date: Wed Jun 21 2017 - 18:21:22 CDT

Dear Josh,

Thanks very much for your detailed explanation. It is helpful to me!
Yeah, I know that it does not matter with Gromacs if I set cutoff-scheme
as Verlet.
I was just curious about it. Thanks!

All the best,
Qinghua

On 06/22/2017 01:02 AM, Vermaas, Joshua wrote:
> What Brian said. :D Fundamentally, charge groups in CHARMM are only defined in the topology file, not the PSF. What topotools does (and has always done) is make a best guess at recapitulating these by keeping track of the total charge sum, and declaring a new charge group once it reaches integer charge (so 0, +1, -1, etc.). For proteins, this heuristic works fairly well, but for things like cyclic sugars, this works much less well, since integer charge usually only comes up once per residue. Happily, this does not matter one iota for newer versions of GROMACS, which don't use charge groups for dynamics.
>
> -Josh
>
> On 06/21/2017 04:57 PM, 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<mailto:brian.radak_at_anl.gov>
> ________________________________
> From: owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu> <owner-vmd-l_at_ks.uiuc.edu><mailto:owner-vmd-l_at_ks.uiuc.edu> on behalf of Qinghua Liao <scorpio.liao_at_gmail.com><mailto: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><mailto: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/topotools9d7e28cd4f5484427885aee7c080%7C1%7C0%7C636336826447728897&sdata=thGcwR3ySy6%2BS%2FDfCTBcRxYUlPJcDK7ELDKQXM2Xgps%3D&reserved=0>
>>
>> ?please let us know, if the ?problem persists.
>>
>> thanks,
>> ? ?
>> ?axel.?
>>
>>
>>
>>> All the best,
>>> Qinghua
>>>
>>
>