[gmx-users] pdb & gro files

Andrea andreamuntean at gmail.com
Fri Mar 5 15:31:48 CET 2010

I don't think the atom number is the problem. I also have systems with more
than 99999 atoms, and in the gro file the atom number after 99999 is reset
to 0, but that was never a problem for the simulations. I would check the
parameters again, but I don't have a more exact answer to your problem.

2010/3/5 Carla Jamous <carlajamous at gmail.com>

> 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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