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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