On 6/03/2010 1:19 AM, Carla Jamous wrote:
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?
Just use .gro files for these intermediate output files. There are very
limited reasons to want .pdb for such intermediate output, such as
visualization. If your visualization program can't read .gro, either get
a new one (e.g. VMD), or use editconf to convert .gro -> .pdb before
visualization.
Mark
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