Hi Nancy, This isn't really a Gromacs related question, and it would be better fit on some chemistry forum. Anyway, whatever answer may come to you, mind that you're interested in the receptor bound form, which may not be what you'll find to be the dominant form. It will depend on the hydrogen bonded network in the pocket. Also, the proton is also probably quite acidic, as the negative charge can delocalize nicely over the ring and the carbonyls, so make sure you're looking at the protonation state too.
Hope it helps, Tsjerk On Mon, Jan 10, 2011 at 12:11 AM, Nancy <nancy5vi...@gmail.com> wrote: > Hi All, > > I am performing molecular docking and molecular dynamics simulations of the > thiazolidinedione pioglitazone binding to the PPAR-gamma receptor protein > (PDB ID: 1ZGY). The thiazolidinedione ring can exist in numerous different > tautomeric states; I have attached a figure depicting several of them. > Which tautomer would be dominant at the physiological pH of ~7.0? > > Also, are there any software programs that can predict which tautomer would > be correct? > > Thanks in advance, > Nancy > > > > -- > 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/Support/Mailing_Lists/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/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
