[gmx-users] Re: converting parmbsc0 dihedrals to RB function

Alan alanwilter at gmail.com
Wed Apr 7 12:11:05 CEST 2010

I strongly advice you to contact Eric Sorin from ffAMBER project as he's
onto that and you maybe can add to his efforts.



On Wed, Apr 7, 2010 at 11:00, <gmx-users-request at gromacs.org> wrote:

> 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.)

Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
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