Hi Lalitha, Zebularine is beyond the trivial. You may be able to derive something reasonable from the other bases using 'chemical intuition' (cytidine, thymidine, uracil), but it's likely that the electronic structure of the ring is too different to justify an approach like that. Likely you should perform parameterization the proper way, which is not a beginners subject. At least have a look at http://www.gromacs.org/WIKI-import/Parametrization
Cheers, Tsjerk On Wed, Oct 14, 2009 at 7:30 AM, lalitha selvam <hayagri...@hotmail.com> wrote: > Hi, > > I want to do simulation with the ligand called zebularine. I dont find > forcefied for that. Also i read prodgr has been deprecated.. > Could you please help me to find out the forcefield for the ligand > zebularine. > Thanks in advance > lalitha > > ________________________________ > Don’t fall behind. Log on to MSN India for a roundup on the world panorama > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > 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 gmx-users-requ...@gromacs.org. > 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://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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
