[gmx-users] pdb2gmx with GROMOS

[Dries Van Rompaey]

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