[gmx-users] which force field for a protein-protein complex?

TJ Piggot t.piggot at bristol.ac.uk
Fri Sep 5 17:01:59 CEST 2008


Personally i would use an AMBER forcefield, because the following link has 
parameters for both the ligands you have in your system, which can be 
tricky and time consuming to derive accurately.


All you need to do is convert the Amber file formats into Gromacs ones, to 
do this by hand consult the Gromacs manual (or you may be able to use the 
ambconv tool which can be found on the user contribution section of the 
Gromacs website).

Also make sure you do not use ffgmx as it is deprecated.


--On Friday, September 05, 2008 15:06:21 +0200 Paula González-Rubio 
<paula.grg at gmail.com> 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
> -- !!!!! NEW email !!!!!!
> paula.grg at univ-paris-diderot.fr
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TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.

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