[gmx-users] conversion of OPLS dihedrals to RB parameters

mernst at tricity.wsu.edu mernst at tricity.wsu.edu
Tue Jan 24 12:16:04 CET 2006


Section 4.58 of the Gromacs manual gives what seems to be a
straightforward method for converting OPLS dihedrals into a representation
using Ryckaert-Bellemans parameters. However, to ensure that I understand
the process, I would like to work through some of the conversions myself.
I am not sure where to find a table or list of OPLS-AA dihedrals given in
their original representation so that I may try to reproduce the
conversion used with Gromacs.

Reference 51 (Jorgensen, W. L., Tirado-Rives, J. The OPLS potential
functions for proteins. energy minimizations
for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110:1657–1666,
1988.) is noted in the manual as if it explains OPLS dihedrals, but this
paper does not go into detail, indicating that OPLS dihedrals are like
AMBER united-atom dihedrals (and this paper itself is about united atom
OPLS). Where can I find the source(s) of OPLS-AA dihedrals in their
original form that were converted to yield the entries in ffoplsaabon.itp?

I am ultimately interested in converting AMBER dihedrals to RB parameters,
for use in conjunction with the AMBER Gromacs port by the Pande group, but
the AMBER dihedral conversion process is simply described as similar to
that for OPLS. I believe I should work through and understand
the process for OPLS first.

Matt Ernst
Washington State University

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