[gmx-users] which force field for a protein-protein complex?
maxfigue at gmail.com
Thu Sep 11 02:55:40 CEST 2008
I was working with protein complex, and after tests some FF, I could obtain
best results with oplss/aa
On Wed, Sep 10, 2008 at 12:07 PM, Alan <alanwilter at gmail.com> wrote:
> Short answer, try Amber99SB with Gaff.
>> Message: 1
>> Date: Fri, 5 Sep 2008 15:06:21 +0200
>> From: " Paula Gonz?lez-Rubio " <paula.grg at gmail.com>
>> Subject: [gmx-users] which force field for a protein-protein complex?
>> To: gmx-users at gromacs.org
>> <2408dbb80809050606k52d73eafsd87f6b54987d6713 at mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>> 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
>> 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
>> 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
>> ******* 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/<
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> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28 <http://www.bio.cam.ac.uk/%7Eawd28><<
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