Hey :) You probably want to fit on the protein and calculate the RMSD on the ligand. You may need to specify these groups in an index file.
Hope it helps, Tsjerk On Mar 27, 2011 3:28 AM, "Justin A. Lemkul" <jalem...@vt.edu> wrote: Nancy wrote: > > Hi All, > > I need to determine the RMSD of a small molecule cocrystallized ligan... I answered this yesterday: http://lists.gromacs.org/pipermail/gmx-users/2011-March/059697.html If there's some reason you can't get that to work, then don't simply re-post the same original question. Iterative calls to g_rms are quite straightforward to script. -Justin > Thank you very much, > Nancy > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://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
