[gmx-users] converting parmbsc0 dihedrals to RB function

[Vigneshwar Ramakrishnan]

Dear Users,



I am trying to port the new parmbsc0 forcefield (
http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0) into gromacs for DNA
simulations.

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
and 180.)



 Any advice or suggestion will be of great help.



Thank you,

Vignesh

-- 
R.Vigneshwar
Graduate Student,
Dept. of Chemical & Biomolecular Engg,
National University of Singapore,
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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