[gmx-users] converting parmbsc0 dihedrals to RB function
vmsrvignesh at gmail.com
Wed Apr 7 11:44:08 CEST 2010
I am trying to port the new parmbsc0 forcefield (
http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0) into gromacs for DNA
While unit conversions are sufficient to convert many of the parameters from
AMBER to GROMACS format, dihedral angle conversion does not seem to be
straight forward - the dihedral parameters need to be converted to the
Ryckaert-Bellemans parameters. I went through the GROMACS 4.0 manual,
especially equations 4.61-4.65 to understand the procedure. The procedure
involves comparing the fourier expansion of the IUPAC convention of dihedral
potential (equation 4.65) with the Ryckaert-Bellemans (RB) functional of
dihedral potential (equation 4.62) to get the Cn's of the RB function.
However, I am not able to understand how to account for the phase angles.
(Also to note, the parmbsc0 forcefield contains phase angles other than 0
Any advice or suggestion will be of great help.
Dept. of Chemical & Biomolecular Engg,
National University of Singapore,
"Strive for Excellence, Never be satisfied with the second Best!!"
I arise in the morning torn between a desire to improve the world and a
desire to enjoy the world. This makes it hard to plan the day. (E.B. White)
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