Hi Tsjerk, Thank you very much for your answer! I use the 43a1 force field. Here are two references of comparative force field studies that suggest that gromos-g96 favours beta sheets. I would be interested in any other study with similar or different conclusions.
Yoda, T.; Sugita, Y. & Okamoto, Y. Secondary-structure preference of force-fields for proteins evaluated by generalized-ensemble simulations Chemical Physics, 2004, 307, 269-283 Yuguang, M.; Kosov, D. S. & Stock, G. Conformational Dynamics of Trialanine in Water. 2. Comparison of AMBER, CHARMM, GROMOS, and OPLS Force Fields to NMR and Infrared Experiments J Phys Chem B, 2003, 107, 5064-5073 Best regards, Pascal > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 20 Feb 2008 20:12:59 +0100 > From: "Tsjerk Wassenaar" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Dose the GROMOS FF favour beta-sheets? > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Pascal, > > Please specify the (Gromos) force field used further. There seems to > be something with the 53a5/6 series in terms of alpha helix / beta > sheet preference. I'm not sure whether this has been fixed already. I > don't recall having heard of such an issue with the 43a2/45a3 series. > But these have there own problems of course, just as any force field > has. Keep up the development! > > Anyway, hope this is useful to you. > > Cheers, > > Tsjerk > > On Feb 20, 2008 5:41 PM, <[EMAIL PROTECTED]> wrote: > > > > Hi everybody, > > > > I am doing some protein unfolding simulations and getting some new, > compact and > > beta-sheet rich unfolded states.I have read 2-3 papers comparing force > fields > > and suggesting that the gromos force field might overstabilize > beta-sheets. Has > > anybody else obtained beta -rich unfolded conformations in protein > unfolding > > simulations, or know of any other relevant reference I might have > overseen? > > > > Thanks a lot in advance!! > > > > Pascal > > > > > > > ******************************************************************************* > > Pascal Baillod (PhD student) > > > ******************************************************************************* > > Swiss Federal Institute of Technology EPFL Tel: > +41-(0)21-693-0322 > > Institute of Chemical Sciences and Engineering , Fax: > +41-(0)21-693-0320 > > Laboratory of Computational Chemistry and Biochemistry > [EMAIL PROTECTED] > > Room BCH 4121, Avenue Forel, > http://lcbcpc21.epfl.ch > > CH-1015 Lausanne > > > ******************************************************************************* > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > 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 gmx-users@gromacs.org 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
