Not 15 minutes ago I sent this response to a nearly identical question...
http://www.gromacs.org/pipermail/gmx-users/2008-September/036259.html
Maybe someone else has some detailed ideas, but I am of the opinion that there
is no substitute for doing your homework about the applicability of protein
force fields to different systems. This can indeed be tricky when you have
ligands present, which is an additional challenge, but there are many options to
get you started (Amber/GAFF, OPLS, PRODRG automation...)
-Justin
Paula González-Rubio wrote:
Hello there,
I would like to do a MD of a protein-protein complex (both with their
ligands) so I'm looking for some advise regarding the best force field
for simulate my system. For more details, it consists on a
ADP-ribosylase (which ligand is the NAD) and a small G protein (GDP
binded), we want to see what is the role of a loop in the formation of
the complex and on the ADP-ribosilation of the small G protein.
Does any one have a good idea of an appropiate force field for this kind
of systems ? Do you think gromos 43A1 or ffgmx could be an option?
Thanks a lot in advance!
Paula
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========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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