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 <[EMAIL PROTECTED]> wrote: > > 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: [email protected] >> 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 <http://www.bio.cam.ac.uk/%7Eawd28><< > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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