marc.lensink at ugent.be
Fri Apr 30 14:44:00 CEST 2004
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 simulation will run fine, if your topology is okay.
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