Hi Subarna, If you just want to retain the structure of the cluster it doesn't matter too much. It may be good to average values from different structures, though. HOWEVER, an FeS cluster is a catalytic site, which probably has fancy electronic properties, which may well affect the behaviour of the surrounding protein. If you are interested in the protein dynamics, you want to describe it properly. Doing so requires proper parameterization, ergo performing quantum mechanical calculations with validation against experimental data, ergo doing a lot of work. This is not something for a lazy Sunday afternoon!
Cheers, Tsjerk On Thu, Jun 25, 2009 at 7:55 AM, subarna thakur<[email protected]> wrote: > Hi everyone > > I am facing a problem with derivation of parameters of Fe-S cluster in a > protein.Can anybody please tell me for deriving a parameters do I have to > consider the co-ordinates of a typical fe-s cluster as there in Protein Data > Base (PDB) or the co-ordinates of the Fe-S cluster present in my protein of > interest. > > > > Subarna > > ________________________________ > ICC World Twenty20 England '09 exclusively on YAHOO! CRICKET > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.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://lists.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
