[gmx-users] pdb & gro files

Mark Abraham Mark.Abraham at anu.edu.au
Sat Mar 6 00:06:33 CET 2010

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 


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