From: Lalit (upmunyu_at_gmail.com)
Date: Tue Jun 07 2011 - 15:12:29 CDT

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

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
>