Short answer, try Amber99SB with Gaff. Alan
> > Message: 1 > Date: Fri, 5 Sep 2008 15:06:21 +0200 > From: " Paula Gonz?lez-Rubio " <[EMAIL PROTECTED]> > Subject: [gmx-users] which force field for a protein-protein complex? > To: gmx-users@gromacs.org > Message-ID: > <[EMAIL PROTECTED]> > 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 !!!!!! > > [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/< > https://paris7.jussieu.fr/Redirect/www.dsimb.inserm.fr/> > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20080905/e69b67f9/attachment-0001.html > > -- -- 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<<
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