[gmx-users] Problems with GROMPP

Jochen Hub jhub at gwdg.de
Fri Jan 11 13:39:43 CET 2008

Jens Pohl wrote:
> Hello!
> I've tried to run GROMPP with a protein, following the flow-chart. Everything is working fine until I try to run the GROMPP program with the *.gro and *.top files I got from GENBOX (spc-water, cubic box, mdp like in the manual). The error is different numbers of coordinates in the two files. What to do??? I re-run the whole cascade several times, everytime ending up with this error.
Some atoms in your gro are probably not listed in the topology. So check 
the number of water molecules, ions, etc and comare with your topology.

To count the number of water molecules, use, e.g.

grep SOL xxx.gro | grep -c OW

Good luck, jochen

> Thanks for you help
> Jens 
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Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de

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