dear all,
in the force field file for residue types ffG53a6.rtp, one of the two
potentials for the so-called "beta" dihedral angle for the nucleic acid
backbone atoms P-O5'-C5'-C4' is missing.
this dihedral potential term is indicated in the article published with
the GROMOS force field 45A4 by Soares et al. 2005 in the Journal of
Computational Chemistry Vol. 26, No.7, pp. 725-737. the parameter set
45A4 is dedicated to nucleic acids, and if i see this correctly, it was
incorporated into the 53A6 force field without further changes.
therefore i suppose this potential was forgotten and should be included
in the force field.
best regards,
daniela
--
Daniela S. Mueller
Biologist (Dipl. Biol.)
Molecular Dynamics (MD)
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
MD group website: http://www.rug.nl/gbb/md
Postal address:
Daniela Mueller
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands
Tel.: +31 (0)50 3634327
Fax.: +31 (0)50 3634398
e-mail: [EMAIL PROTECTED]
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