Thanks, I'll try that, and post again if it works. On Mon, Sep 12, 2011 at 6:20 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Shay Teaching wrote: > >> 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? >> > > Are there chain identifiers separating the proteins? I don't know if that > would cause the problem, but it's possible. In that case, I'd suggest you > start with a coordinate file and topology without chain identifiers and > generate a new .tpr file (and then take the backbone atoms only with > tpbconv). > > -Justin > > Thanks again, >> -Shay >> >> >> On Mon, Sep 12, 2011 at 5:29 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> 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 <http://vt.edu> | (540) 231-9080 >> <tel:%28540%29%20231-9080> >> >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >> >> <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 >> <mailto:gmx-users@gromacs.org> >> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> <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> >> >> <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 >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> >> Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> > -- > ==============================**========== > > 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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