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

[Maximiliano Figueroa]

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.
>
> Alan
>
>>
>> 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
>> Message-ID:
>>        <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
>> (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
>>
>>
>> ******* NEW ADDRESS ******
>> Paula GONZALEZ-RUBIO
>> PhD Candidate
>> DSIMB INTS, INSERM UMR-S726
>> 6 rue Alexandre Cabanel 75015 Paris
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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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