[gmx-users] Blank Coordinate File

[Souparno Adhikary]

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.