Dear Justin, Thanks for your reply. Well, to explore the effect of the ligand on protein
g_mindist -f run.xtc -s run.tpr -od mindist.xvg -on numcont.xvg Select a group: 1 Selected 1: 'Protein' Select a group: 13 Selected 13: 'LİGAND' Does this choice make sense? 30 Haziran 2011 14:43 tarihinde Justin A. Lemkul <[email protected]> yazdı: > > > ahmet yıldırım wrote: > >> Dear users, >> >> I want to see the effect of the ligand on each residue using the following >> command: >> g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res >> >> Select group(s) for root mean square calculation >> Select a group: ? >> Which group should I choose? >> >> > The group that is most meaningful to you, based on the behavior observed in > the trajectory. You can analyze backbone, sidechain, or all protein atoms > separately. Several iterations may be informative, using several different > groups. > > -Justin > > -- > ==============================**========== > > 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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 [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Ahmet YILDIRIM
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