[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.

[Justin Lemkul]

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================