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
