VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Wed Apr 21 2004 - 15:47:17 CDT

davide,

try using the preprocessed topology file,
i.e. the one you get from using grompp's -pp option.

axel.

On Wed, 21 Apr 2004 13:40:22 -0500 John Stone wrote:

>
> Davide,
> I'd suggest emailing Marc Baaden and see if he has a suggestion since
> he's the one that wrote the script. I don't personally know anything
> about Gromacs yet, but if that doesn't pan out, the next option would be
> for someone to write a real Gromacs .top reader plugin for VMD, which is
> probably the best long-term solution. Marc's email is on that top2psf page
> I sent previously.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Apr 21, 2004 at 01:04:51PM +0200, davide.ruffoni wrote:
> > Hi, I'm using top2psf script. The problem is that the waters molecules inserted
> > by gromacs in the topology file (.top) are not converted in the psf, thus when
> > I try to merge the coordinates (coor.trr) with the topol.psf I get as error:
> > incorrect number of atom. How to solve this problem?
> > Thanks in advance
> > Davide
> >
> >
> >
> >
> > --
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> 

--
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Axel Kohlmeyer      e-mail:  axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum                   http://www.theochem.ruhr-uni-bochum.de
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.