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

Henrik Rundgren henrik at physc.su.se
Fri Apr 30 14:39:01 CEST 2004

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?

WILL this cause me any problems when I analyze the results later (or 
force me to make index files manually), because I can't see any proplems 
running the simulation. I test ran it for a while, and it seemed ok.
I have searched the mailing list, not found a satisfying answer for this.


Henrik Rundgren
Division of Physical Chemistry
Arrhenius Laboratory
Stockholm University
S-106 91 Stockholm

E-mail:    Henrik at physc.su.se
Telephone: +46-(0)8-16 12 63
Fax:       +46-(0)8-15 21 87
Website:   www.fos.su.se/~henrik

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