On 6/12/17 4:58 PM, Rana Rehan Khalid wrote:
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
pdb2gmx is just being verbose regarding changes made to termini (patching).
Note that the program tells you it successfully generated the topology.
-Justin
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
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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