[gmx-users] pdb2gmx with GROMOS

[Marco Franzoi]

You can try to add the -ter flag to pdb2gmx and manually select the n and c
ter.

Best,
Marco

Marco FRANZOI
PhD Student
University of Padua
Department of biology, V floor South
Tel: 3405086908
Mail: marco.franzoi89 at gmail.com

On Tue, Jan 19, 2016 at 4:26 PM, Dries Van Rompaey <
dries.vanrompaey at gmail.com> 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?
>
> Thanks in advance,
>
> Dries
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