[gmx-users] water clusters MD

Oleksandr nablaoblada at yahoo.com
Mon May 31 10:45:35 CEST 2010

I'm new user of Gromacs. There are plenty examples how to do solvation study of various proteins. But I'd like to "solvate" highly ordered heavy water clusters in box of light water. At the first step when I execute  "pdb2gmx -f watercluster.pdb" I get an error no matter which model is chosen:

Fatal error:
Atom H in residue HOH 4 not found in rtp entry with 3 atoms
             while sorting atoms. Maybe different protonation state.
             Remove this hydrogen or choose a different protonation state.
             Option -ignh will ignore all hydrogens in the input.

Can anybody help me how to solve this problem?
Thanks a lot


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