Ok I tried that and it doesn't work: There's a fundamental difference between chains/no-chains topology, namely the existence of peptide bond between chains, and the different protonation state on the termini. In the chain-based topology there are several termini, and less peptide bonds.
This causes the no-chains-tpr to have different number of atoms, and different protonation states. I tried using tpbconv to make a backbone-tpr, but it still gets me to segmentation fault. So thanks, but I don't think it would work. -SA On Mon, Sep 12, 2011 at 11:47 PM, Shay Teaching <shay.teach...@gmail.com>wrote: > 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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