[gmx-users] which force field for a protein-protein complex?
Justin A. Lemkul
jalemkul at vt.edu
Fri Sep 5 15:19:51 CEST 2008
Not 15 minutes ago I sent this response to a nearly identical question...
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...)
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!
> -- !!!!! NEW email !!!!!!
> paula.grg at univ-paris-diderot.fr <mailto:paula.grg at univ-paris-diderot.fr>
> ******* NEW ADDRESS ******
> Paula GONZALEZ-RUBIO
> PhD Candidate
> DSIMB INTS, INSERM UMR-S726
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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