[gmx-users] gromacs warning topology file naming residues

[Justin Lemkul]

On 5/5/16 6:18 AM, Upasana Ray wrote:
> Dear user
>
> During energy minimization of my modelled and loop optimized protein
> I am getting two warning as following..I am working in ffg53a5 force filled
> with spc216 water model in version 5.0.7
>

53A5 was parametrized for use in nonpolar solvents; it is not a good choice for 
aqueous solution.

> 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 318 named ASP 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.
>

Unfortunately, you haven't shown us your pdb2gmx command or subsequent screen 
output, but suffice it to say that you're not treating the termini correctly. 
Usually these errors show up when the user has incorrectly chosen "None" as the 
termini.

-Justin

-- 
==================================================

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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