I strongly advice you to contact Eric Sorin from ffAMBER project as he's onto that and you maybe can add to his efforts.
http://ffamber.cnsm.csulb.edu/ Alan On Wed, Apr 7, 2010 at 11:00, <gmx-users-requ...@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. >>http://www.bio.cam.ac.uk/~awd28<<
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