Dear Justin, I used -res flag with the following command but I get pairs of values in the output files. is there any mistake related with the command I used? g_rmsf -s run.tpr -f run.xtc -o rmsf.xvg -od rmsdev.xvg -res
2011/5/29 <jalem...@vt.edu> > Quoting ahmet y?ld?r?m <ahmedo...@gmail.com>: > > Dear Justin, >> >> You said " You can get a per-residue RMSD by using g_rmsf -od to see the >> effect of the ligand on each residue." >> 1. Can you explain the difference between what goes into the -o file, and >> what goes into the -od file? >> > > The -o output is RMSF; the -od output is RMSD. > > > 2. How should I create a index file to see the effect of the ligand on >> each >> residue? Do I have to create the index file? >> g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg >> Is this command sufficient to see the effect of the ligand on each >> residue? >> > > An index file should not be necessary. By default, the output is per atom, > so use the -res flag if you want the measurements averaged over all atoms in > each residue. The command is sufficient to measure the RMSD per residue. > Whether or not that is sufficient is up to you. > > 3. Furthermore, can you suggest the other analysis tools to see the effect >> of the ligand *on protein*? >> >> > You should identify the quantities you wish to measure, then read in the > Gromacs manual about the different utility programs available. You'll learn > far more that way. > > -Justin > > > Thanks in advance >> >> 2011/5/28 <jalem...@vt.edu> >> >> Quoting ahmet y?ld?r?m <ahmedo...@gmail.com>: >>> >>> Dear users, >>> >>>> >>>> I want to investigate *Ligand effect *on the protein . >>>> To investigation the interaction of protein-ligand: >>>> *RMSD calculations:* >>>> 1. >>>> a) RMSD of Backbone >>>> b) RMSD of Backbone+ligand >>>> 2. >>>> a) RMSD of Protein >>>> b) RMSD of Protein+ligand >>>> 3. >>>> a) RMSD of Protein-H >>>> b) RMSD of Protein-H+ligand >>>> Which one would you recommend ( 1., 2., and 2.choice)? >>>> >>>> >>>> Unless the effect of your ligand is very large (i.e., the whole protein >>> is >>> significantly more or less stable in the presence of the ligand), then >>> likely none of these analyses will be particularly illustrative as they >>> are >>> not very sensitive to small changes. You can get a per-residue RMSD by >>> using g_rmsf -od to see the effect of the ligand on each residue. >>> Otherwise, the most common quantity measured is backbone RMSD. >>> >>> -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 >>> >>> ======================================== >>> -- >>> 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 thewww >>> interface >>> or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> >> >> >> -- >> Ahmet YILDIRIM >> >> > > > -- > ======================================== > > 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 thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Ahmet YILDIRIM
-- 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