[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]

thanks Justin

it means I can move forward  to next steps of simulation

On Mon, Jun 12, 2017 at 4:59 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
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