[gmx-users] WARNING: WARNING: Residue 1 named MET 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.

[Rana Rehan Khalid]

hi Justin
i am working on heme FE containing protein i used GROMOS96 53a6 force field
for making topology file the warnings shows but parameter file created
complete. i want to know that this force field is right to run simulation
for fe heme containing protein. here is the warning kindly guide me how can
i remove these warning


WARNING: WARNING: Residue 1 named MET 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 186 named SER 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: 3157 pairs
Before cleaning: 3852 dihedrals
Making cmap torsions...
There are 1027 dihedrals, 1020 impropers, 2936 angles
          3157 pairs,     2001 bonds and     0 virtual sites
Total mass 21951.823 a.m.u.
Total charge -14.000 e
Writing topology

Back Off! I just backed up posre.itp to ./#posre.itp.1#

Writing coordinate file...

Back Off! I just backed up hnox_processed.gro to ./#hnox_processed.gro.1#
        --------- PLEASE NOTE ------------
You have successfully generated a topology from: hnox.pdb.
The Gromos53a6 force field and the spce water model are used.
        --------- ETON ESAELP ------------

gcq#191: "Take Dehydrated Water On Your Desert Trips" (Space Quest III)


regards
ray