[gmx-users] converting parmbsc0 dihedrals to RB function

Mark Abraham Mark.Abraham at anu.edu.au
Wed Apr 7 16:04:01 CEST 2010

On 7/04/2010 7:44 PM, Vigneshwar Ramakrishnan wrote:
> 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.

Why? GROMACS can probably do the non-RB form - IIRC you can implement a 
sum of multiple instances of 4.61 with different n.

> 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.)

Elegant conversion formulae require those angles to be convenient...


>   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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