[gmx-users] Problem???!!?

[Marc Lensink]

On Friday 30 April 2004 12:38, Henrik Rundgren wrote:
> Hi all.
> I am doing a simulation on a cyclic peptide, with unusual a.a's.
> They are included in the *.rtp file, and in aminoacids.dat a.s.o
> But when I run grompp it will not report them to be a part of the
> protein.. Only the "regular" residues are included as PROTEIN
> residues, the rest to OTHER residues... WHY?

There's probably a file in the $GMXDATA/top/ directory that identifies
which residues are PROTEIN residues.

Change this file, or simply make an index file manually. I'd suggest
the latter.

The simulation will run fine, if your topology is okay.

Marc