We were trying to solvate a small peptide (octamer) in water to run a 100ns simulation of it.
In the pdb2gmx step, we have provided -ignh and -ter options (with NH3+ and COO-) and used the gromos53a6 forcefield. It did not generate any error. But it is generating a blank coordinate file (.gro). Here is the output of the pdb2gmx command:- End terminus ARG-9: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 8 residues with 139 atoms Making bonds... Number of bonds was 143, now 138 Generating angles, dihedrals and pairs... WARNING: WARNING: Residue 1 named ARG of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 8 named ARG of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 238 pairs Before cleaning: 238 dihedrals Making cmap torsions... There are 79 dihedrals, 55 impropers, 195 angles 238 pairs, 138 bonds and 0 virtual sites Total mass 1275.585 a.m.u. Total charge 8.000 e Writing topology Back Off! I just backed up posre.itp to ./#posre.itp.2# Writing coordinate file... Back Off! I just backed up polyr.gro to ./#polyr.gro.2# --------- PLEASE NOTE ------------ You have successfully generated a topology from: polyr.pdb. The Gromos53a6 force field and the spc water model are used. --------- ETON ESAELP ------------ gcq#415: "In a talk you have a choice: You can make one point or no points." (Paul Sigler) Any help??? Please??? Souparno Adhikary, CHPC Lab, Department of Microbiology, University of Calcutta. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.