Hi Ramon, Zinc should be considered as one of those "exotic species" (http://wiki.gromacs.org/index.php/Exotic_Species). It's almost impossible to give a set of parameters which will work for all zinc binding sites. Actually, it's best to parameterize based on the environment. Now, if you have QM/MM calculations, I think it should be possible to use these to fit parameters. As for the literature, I believe I had some references to zinc parameterization in our Proteins paper (TRAIL-DR5 complex) from earlier this year.
Hope it helps, Tsjerk On Thu, Jul 17, 2008 at 12:15 PM, Ramon Crehuet <[EMAIL PROTECTED]> wrote: > Dear Gromacs users, > I am planing to do MD of an enzyme that has a Zn in its active site. Up > to now I have used QM/MM or ONIOM approaches but now I need to perform a > long MD and would like to model the Zn with MM, preferably in OPLS. > I know that there are three possible approaches: Bonded, nonbonded and > cationic dummy atom. I have seen a thread, where Maik Goette said that > onyl the bonded approach worked. I would like to know in more detail > what kind of problems could I encounter. What does "not work" imply? > Weeks of unreliable calculations...? > I would also be very grateful if people working in this area could send > me some reference publications, in particular of what can be done with > Gromacs. I have only found: "Zinc binding in proteins and solution: A > simple but accurate nonbonded representation" Roland H. Stote, Martin > Karplus, 1995. > Thanks in advance, > Ramon > _______________________________________________ > 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
