[gmx-users] Problems with GROMPP

[Jens Pohl]

> -----Ursprüngliche Nachricht-----
> Von: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Gesendet: 11.01.08 13:41:35
> An: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Betreff: Re: [gmx-users] Problems with GROMPP
> 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 

Thank you for your help!

It seems, that my protein is truncated in the xxx.gro file. The number of water molecules is ok, but there are about 150 AS residues missing after I run GENBOX ??? The xxx.top has them included, so this explains the different numbers.

Jens

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