[gmx-users] (no subject)

Fernando Mattio mattiofer at gmail.com
Fri Oct 7 13:29:25 CEST 2005

Dear Gromacs users,

I had a box with a solvated protein (minimized_water.gro) and used the
genconf to generate another box of protein surrounded by water (I duplicated
it). Well I could notice in the VMD that the .gro file generated
(minimized_2water.gro) really represents what I tried to do, but when I
tried to run a simulation I had the following fatal error:
Fatal error: number of coordinates in coordinate file (minimized_2water.gro,
does not match topology (aki.top, 31372)

It is clear for me that the topology file was not updated, I mean it
represents the first .gro file...
So what should I do to update my .top file to run a simulation? I thought
about using the prodrg serve, but what I understood is that this server
generates topologies from pdb files, what is not the case.

Many thanks in advance,
Fernando Mattio
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