On 2012-01-29 07:20, James Starlight wrote:
Dear Gromacs USers!
I'm looking for good force field for the simulation of the
protein-ligand complex in vacuum.
In accordance to the Justin's tutorial I've found that GROMOS96 43b1
force field might be good choice for that task.
But my version of GROMACS lack for that force field .rtps :(
Because that ff is not well-documented, the only difference with the
normal gromos43 force field is that the side chains are neutral.
Please check this paper for a comparison of FF for vacuum simulations:
Erik Marklund, Daniel Larsson, Alexandra Patriksson, David van der Spoel
& Carl Caleman: Structural stability of electrosprayed proteins:
temperature and hydration effects Phys. Chem. Chem. Phys. 11 pp.
8069-8078 (2009)
Could you tell me where I could dwnload this force fields parameters?
Thanks,
James
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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