Hi Nahren, You probably used make_ndx for making the index file. Unfortunately it sorts the indices. You have to construct it in such a way that that the indices are in the order you want them. You can script the generation, based on the chain ID, or you can make separate index files that you concatenate together. In the latter case, do mind to remove the index group tags that are placed at the top of each file and add such a tag at the top of the concatenated file.
Cheers, Tsjerk On Tue, May 11, 2010 at 3:35 PM, nahren manuel <meetnah...@yahoo.com> wrote: > Dear Tsjerk, > The trjconv is not working, it is likely that i am not issuing the proper > commands. > > > --- My ndx file - - - > Select group for output > Group 0 ( System) has 2619 elements > Group 1 ( Protein) has 2619 elements > Group 2 ( Protein-H) has 2619 elements > Group 3 ( C-alpha) has 873 elements > Group 4 ( Backbone) has 2619 elements > Group 5 ( MainChain) has 2619 elements > Group 6 (MainChain+Cb) has 2619 elements > Group 7 ( MainChain+H) has 2619 elements > Group 8 ( SideChain) has 0 elements > Group 9 ( SideChain-H) has 0 elements > Group 10 (r_1-152_r_457-595) has 873 elements > Group 11 (r_153-304_r_596-734) has 873 elements > Group 12 (r_305-456_r_735-873) has 873 elements > Group 13 ( a_1-456) has 456 elements > Group 14 (a_1-456_a_1369-1785) has 873 elements > Group 15 (a_457-912_a_1786-2202) has 873 elements > Group 16 (a_913-1368_a_2203-2619) has 873 elements > Group 17 > (a_1-456_a_1369-1785_a_457-912_a_1786-2202_a_913-1368_a_2203-2619) has 2619 > elements > > > Kindly advice > nahren > > --- On *Mon, 5/10/10, nahren manuel <meetnah...@yahoo.com>* wrote: > > > From: nahren manuel <meetnah...@yahoo.com> > > Subject: Re: [gmx-users] Trj conversion: ABCXYZ to AXBYCZ > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Date: Monday, May 10, 2010, 3:50 PM > > > Dear Tsjerk, > > No the problem was not with GROMACS. I have one structure as a X-ray and > the other i created by homology modeling based on this structure. So the > difference arose because my starting structures themselves were different. > > I did try trjconv with an index file , but it did not work out fine. I will > check them once again before getting back. > > Thank you > > nahren > > --- On *Mon, 5/10/10, Tsjerk Wassenaar <tsje...@gmail.com>* wrote: > > > From: Tsjerk Wassenaar <tsje...@gmail.com> > Subject: Re: [gmx-users] Trj conversion: ABCXYZ to AXBYCZ > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Date: Monday, May 10, 2010, 3:35 PM > > Hi Nahren, > > You can do that using trjconv and an index file with the atom indices as > they are in the order as they have to be. > > But is that really your problem? To understand what happened, it would help > if you gave the series of commands that led to these results. > > Cheers, > > Tsjerk > > On Mon, May 10, 2010 at 11:42 AM, nahren manuel <meetnah...@yahoo.com>wrote: > >> Dear Gromacs Users, >> >> I simulated two homologous (proteins) , and noticed after the simulation >> that in one trajectory, the protein is stored as ABCXYZ and in another it is >> as AXBYCZ. (where A, Z are chain information, ABC is a trimer and XYZ is >> another trimer, so the system is a trimer-trimer complex) >> >> >> I should not have any issues for most of my trajectory analysis. But >> when I wanted to get a correlation plots of the CA-CA from the covariance >> matrix, the plots cannot be compared, as the information in the trajectory >> is different. >> >> >> So is there a way that I can convert my trajectory from ABCXYZ to >> AXBYCZ. >> >> >> Thank you, >> >> nahren >> >> >> -- >> 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/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/mailing_lists/users.php >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > Groningen Institute for Biomolecular Research and Biotechnology > University of Groningen > The Netherlands > > -----Inline Attachment Follows----- > > -- > 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/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/mailing_lists/users.php > > > > -----Inline Attachment Follows----- > > -- > gmx-users mailing list > gmx-users@gromacs.org<http://mc/compose?to=gmx-us...@gromacs.org> > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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<http://mc/compose?to=gmx-users-requ...@gromacs.org> > . > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > -- > 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/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/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands
-- 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/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/mailing_lists/users.php