[gmx-users] pdb & gro files

[Carla Jamous]

Hi,
please I'm having a problem while running a minimisation.

I prepared my system with pdb2gmx and generated .pdb files. From the last
pdb file, I did grompp & generated the tpr file that I used to start my
minimization. At the 46th step, I encountered the problem:"water molecule
cannot be settled".
I looked at the pdb file and found that many water residues have the same
number because above residue 9999, it restarts to count residue 0, 1, etc...

I prepared the same system but I generated .gro files instead of .pdb &
started my minimization. But did't encounter the same problem.
I looked at the gro file & here, it's the atomic number that can't be above
99999.

So did anyone encounter this problem before, & if yes, please do you have a
solution to propose?

Thanks

Carla
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