[gmx-users] pdb2gmx with GROMOS

[Justin Lemkul]

On 1/19/16 10:26 AM, Dries Van Rompaey wrote:
> Dear gmx-users,
>
> I'm experiencing the following warning while running pdb2gmx (gmx pdb2gmx
> -f 1AKI.pdb), selecting any of the GROMOS force fields; all others work
> fine. I get the same error with the -ignh flag.
>
> WARNING: WARNING: Residue 1 named LYS 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 129 named LEU 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.
>
> I'm using gromacs 5.1.1 on mac os x. I looked at the rtp and
> aminoacids.c.tbd/aminoacids.n.tbd files in top/gromos54A7, but I couldn't
> discover any discrepancies. I also checked the angles in the topology, but
> it looks like everything that should be applied, based on the contents of
> the aminoacids.c.tbd/aminoacids.n.tbd files, seems to be applied.
>
>   The system I'm working on is lysozyme (pdb code 1AKI). I'm assuming the
> root cause of this warning is located somewhere in the
> aminoacids.c.tbd/aminoacids.n.tbd files, as both residues are terminal
> residues.
>
> Can anyone replicate these warnings or does anyone know where they come
> from?
>

What did you choose for the termini?  From the warnings, it looks like you chose 
"None," which is not appropriate.  The .tdb files should be overriding standard 
residue atom naming in the case of properly chosen 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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