When I try to work the command on a small portion of the backbone it seems to work just fine. But when I try the entire backbone (which is composed of several *separate* chains) I am getting segmentation fault. Any workaround for that, so I can use the entire backbone? Thanks again, -Shay
On Mon, Sep 12, 2011 at 5:29 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Shay Teaching wrote: > >> Hi all, >> (Gromacs 4.0.7): I am trying to make rms matrix between one Wt trajectory >> and one mutant trajectory using the following command: >> >> g_rms -f wt.xtc -f2 mutant.xtc -s wt.tpr -m -fit rot+trans -n >> wt_backbone.ndx >> >> The file wt_backbone.ndx contains the backbone of the protein (Backbone >> indices are identical between wt and mutant). >> >> The result is that I am getting a well deserved error saying that wt.xtc >> and mutant.xtc has different number of atoms (the tpr itself): >> Fatal error: >> Second trajectory (76128 atoms) does not match the first one (76129 atoms) >> >> So the question becomes: Is there a (convenient) way to produce rms-matrix >> between wt and mutant? >> Or perhaps circumvent this problem in some other way? >> > > Use trjconv to write out new trajectories containing only backbone atoms of > each protein, then use tpbconv to write a .tpr file with only backbone atoms > in it (using index groups, if necessary). Then run g_rms again with these > new trajectories and .tpr file. Everything should match if the indices are > chosen correctly. > > -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 gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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