Hi,
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.
http://www.pharmacy.manchester.ac.uk/bryce/amber
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.
Tom
--On Friday, September 05, 2008 15:06:21 +0200 Paula González-Rubio
<[EMAIL PROTECTED]> 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 !!!!!!
[EMAIL PROTECTED]
******* NEW ADDRESS ******
Paula GONZALEZ-RUBIO
PhD Candidate
DSIMB INTS, INSERM UMR-S726
6 rue Alexandre Cabanel 75015 Paris
Tel : +33(1) 44 49 30 00 Fax : +33(1) 47 34 74 31
4th Floor. Room 401 Bis
Web Site: http://www.dsimb.inserm.fr/
----------------------
TJ Piggot
[EMAIL PROTECTED]
University of Bristol, UK.
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