[gmx-users] pdb & gro files

Carla Jamous carlajamous at gmail.com
Fri Mar 5 15:19:20 CET 2010

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

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


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100305/cdccb9f4/attachment.html>

More information about the gromacs.org_gmx-users mailing list