[MMTK] Groups "ace_beginning_nt" and "nmethyl_ct" defined in MMTK/Database

Berit Hinnemann Berit.Hinnemann@fysik.dtu.dk
Mon, 23 Jul 2001 16:56:50 +0200

Hi all,

I guess this is mainly a question to Konrad, but I thought it might be
interesting to the others as well.

The two groups "ace_beginning_nt" and "nmethyl_ct" defined in
MMTK/Database are used for
N- and C-termination of the protein "bala1" (also used in the MMTK
examples). I consider using them to terminate a peptide chain nicely in
both ends, i.e. without charges. My goal is to simulate long chains so
that I can eliminate the influence of the termination, thus I am just
looking for some nice termination.

My question is, are the AMBER force field parameters assigned to both
groups realistic? As these groups are only used for the toy-protein
bala1 in the examples, I just want to confirm that the parameters were
taken out of AMBER.

Thanks a lot,

Berit Hinnemann, Dipl.-Phys.
Center for Atomic-Scale Materials Physics (CAMP)
Dept. of Physics, Technical University of Denmark
Building 307, DK-2800 Lyngby, Denmark 
Phone: +45 4525 3209, Fax: +45 4593 2399