[gmx-users] which force field for a protein-protein complex?
tsjerkw at gmail.com
Thu Sep 11 10:10:00 CEST 2008
Could you give some more argumentation regarding your choice of
opls-aa? What tests did you use and what were your criteria? Did you
verify against experimental data?
I wouldn't go for Gromos 43a1 and most certainly not for ffgmx. The
latter is completely obsolete, and the former likely should share that
qualification. It's superseded by their newer force fields, 43a2/45a3
and 53a5/53a6. The last two of these are the result of a new
philosophy behind the parameterization. Check the papers if you want
to know more.
Since you're dealing with ligands of which I'm not sure whether the
(newer) GROMOS force fields can handle them correctly, maybe Alan's
suggestion to try Amber/Gaff is not so bad.
Hope it helps,
On Thu, Sep 11, 2008 at 2:55 AM, Maximiliano Figueroa
<maxfigue at gmail.com> wrote:
> 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
>>> 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
>>> 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
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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.
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
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