[gmx-users] beta dihedral potential for nucleic acid backbone missing in force field file

Daniela S. Mueller d.s.mueller at rug.nl
Fri Mar 23 15:40:24 CET 2007

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 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: d.s.mueller at rug.nl

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