VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Jun 06 2011 - 18:26:46 CDT

lalit,

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.

yes, this is definitely a deficiency of topotools _not_ gromacs.
the "fake topology" output is pretty crude and nobody has yet
run into this problem. i'll have a look at what can be done.

more later,
    axel.

> 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

thanks, this is very helpful. a.

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