VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jun 07 2011 - 15:24:30 CDT

On Tue, Jun 7, 2011 at 4:12 PM, Lalit <upmunyu_at_gmail.com> wrote:
> Hello Axel,
>
> Yes, that worked! Thanks!!
>
> The generated {.top} as well as {.tpr}  files are suitable to use for
> analysis.
>
> Moreover, one may please check the response I got from gromacs-mailing list
> (especially about the number of atoms ought to be there in a charge group
> based upon functional group):
>
> http://lists.gromacs.org/pipermail/gmx-users/2011-June/061989.html

the top file that is generated is deliberately set up so that
it will generate complete nonsense if run as a real MD.

so, as justin pointed out, it doesn't matter for analysis,
it just needs to be set up in a way so that it generates
a usable tpr file. right now the heuristics are set up to
generate charge groups that are either neutral or have
an integer charge. that may turn out to be helpful for
some -- currently not existing -- analysis. but it also
enforces the required limit.

i think this is good enough. just arbitrarily choosing
a few atoms, may be more difficult, particularly in
the way you have ordered the atoms. having to do
reordering would be much worse.

cheers,
    axel.

>
> Thanks again,
> --- Lalit
>
>
>
>
> On Mon, Jun 6, 2011 at 7:14 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> lalit,
>>
>> i just posted a new version of the topotools plugin at this URL.
>>
>>
>> http://sites.google.com/site/akohlmey/software/topotools/topotools-1.2-20110606.tar.gz
>>
>> please follow the installation instructions at:
>>
>> http://sites.google.com/site/akohlmey/software/topotools/
>>
>> this should avoid the problem that you are seeing.
>> please try it out and let us know.
>>
>> thanks,
>>    axel.
>>
>> On Mon, Jun 6, 2011 at 7:19 PM, Lalit <upmunyu_at_gmail.com> wrote:
>> > Hi All,
>> >
>> > I am interested in using gromacs utilities for analysis with {.dcd,
>> > .psf}
>> > files. One do need to have {.tpr} file for some tools, eg., for
>> > g_density.
>> >
>> > I am following this link from NAMD mailing list:
>> >
>> > http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/14046.html
>> >
>> > As suggest, by Axel, I was able to get the {.top} file.
>> >
>> > However, when I used gromacs's "grompp" command:
>> >
>> > $ grompp -f minim1.mdp -c BL1_only.pdb -p BL1_only.top -o BL1_only.tpr
>> >
>> > I was returned with an error like this:
>> >
>> > -------------------------------------------------------
>> > Program grompp, VERSION 4.5.4
>> > Source code file:
>> > /home/mandrake/rpm/BUILD/gromacs-4.5.4/src/kernel/grompp.c, line: 175
>> >
>> > Fatal error:
>> > The largest charge group contains 140 atoms. The maximum is 32.
>> > For more information and tips for troubleshooting, please check the
>> > GROMACS
>> > website at http://www.gromacs.org/Documentation/Errors
>> > -------------------------------------------------------
>> >
>> > I am searching gromacs mailing list and still looking for an answer. I
>> > am
>> > also asking them about this error.
>> >
>> > However, I feel like, is there something can be done on {.top}
>> > generating
>> > step? I tend to think to resolve this error more through NAMD/VMD point
>> > of
>> > view rather then going deep into Gromacs way of thinking and de-bugging.
>> >
>> > Please suggest and help.
>> >
>> > Thanks a lot,
>> > --- Lalit
>> >
>> > p.s.: All relevant files: BL1_only.pdb; BL1_only.psf; BL1_only.top &
>> > minim1.mdp can be downloaded from:
>> >
>> > http://lalitpkc.phy.uic.edu/~lalit/GROMACS_files
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.