Dear Justin, Thanks for your immediate reply.
Is it possible to do clustering based on side-chain RMSF in gromacs? What about dihedral angle order parameters in gromacs?. Does it provide any information about what I want to know? Thanking you once again regards Anu On Mon, Apr 1, 2013 at 8:28 PM, Justin Lemkul <jalem...@vt.edu> wrote: > On Mon, Apr 1, 2013 at 4:52 AM, anu chandra <anu80...@gmail.com> wrote: > > > Dear amber users, > > > > I am working with protein-ligand interaction. The protein shows high > degree > > of side-chain conformational changes and minimal backbone conformational > > changes during ligand binding. In order to capture these side chain > > flexibility, as a initial step, I would like to do clustering based on > the > > side-chain flexibility (i.e. categorise different areas in protein based > on > > the degree of side chain flexibility). Is there a way to do such a > > calculation in Gromacs?. Can any one suggested me a way to proceed with > > this sort of analysis? > > > > > g_cluster does RMSD-based clustering. That's not "flexibility" per se, but > might be informative. If you do fitting based on side chains (which might > be difficult, since side chains flop around a lot), that's about as close > to achieving what you're after as I can think of using standard Gromacs > programs. > > -Justin > > -- > > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) > 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 > -- 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
