Maximiliano, 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?
Paula, 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 It's superseded by their newer force fields, 43a2/45a3 and 53a5/53a6.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, Tsjerk On Thu, Sep 11, 2008 at 2:55 AM, Maximiliano Figueroa <[EMAIL PROTECTED]> 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 <[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<< >> >> _______________________________________________ >> 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 > > > _______________________________________________ > 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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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
