Re: [gmx-users] Covariance analysis of X-ray ensemble
Hello. Check your topology file. You should have had a mistake in matching the atoms. Best regards. Lucio. El vie, 11-01-2013 a las 21:46 +0300, James Starlight escribió: Tsjerk, thanks for suggestion! By the way I've found in the pca.log ( that time pca was done on trajectory as well as TRP ( not pdb) files as the inputs ): Read 30 frames from cam_xray_coors_bb.pdb (time 1 to 30 ps) Read reference structure for fit from x_ray.tpr Analysis group is 'System' (575 atoms) Fit group is 'System' (575 atoms) Analysis is non-mass weighted Fit is non-mass weighted Diagonalized the 1725x1725 covariance matrix Trace of the covariance matrix before diagonalizing: 350.847 Trace of the covariance matrix after diagonalizing: 350.847 Wrote 1725 eigenvalues to PCA_eigenval.xvg Wrote reference structure to PCA_eigenvec.trr Wrote average structure to PCA_average.pdb and PCA_eigenvec.trr Wrote eigenvectors 1 to 29 to PCA_eigenvec.trr It seems that cov.analysis was done also as non-mass weighted. Actualy I extract eigenvectors for further essential dynamics sampling runs. In the literature I've found that for EDA eigenvectors from only non-mass weighted PCA are suitable. So if its true in what cases mass weighted eigenvectors might be used? James 2013/1/11 Tsjerk Wassenaar tsje...@gmail.com: Hi James, You don't need a .tpr file. A .gro or .pdb file will do as well. Unless you insist on doing mass-weighted PCA. Cheers, Tsjerk On Fri, Jan 11, 2013 at 4:04 PM, James Starlight jmsstarli...@gmail.comwrote: Dear Gromacs users! I want to perform Covariance analysis of my x-ray data sets via g_covar -f trr.pdb -s x_ray.tpr -n index -o PCA_eigenval.xvg -v PCA_eigenvec.trr where trr.pdb is the trajectory made from the 30 x-ray structures (only c-alpha atoms were selected. How I could obtain x_ray.tpr file for such analysis? I've tried to use tpr from full atomic model of the same protein which I';ve simulated recently. For that p[rotein tpr file have been already created. From that model via make_ndx I've defined only backbone atoms corresponded to the atoms in my pdb ensemble. On the next step I've used tpbconv on protein.tpr with index file to make reduced tpr file with atoms corresponded to the backbone of the pdb-ensemble. Now when I run g_covar with my ensemble and reduced tpr file I obtain error *** glibc detected *** g_covar: malloc(): memory corruption: 0x7f27df53e018 *** On other hand if I specify for g_covar full-atomic tpr file with the index ( where atoms corresponded to the trr.pdb are mentioned) g_covar -f trr.pdb -s protein.tpr -n index -o PCA_eigenval.xvg -v PCA_eigenvec.trr I obtain another error Calculating the average structure ... Reading frame 0 time1.000 WARNING: number of atoms in tpx (575) and trajectory (575) do not match --- Program g_covar, VERSION 4.5.5 Source code file: /tmp/build/gromacs-4.5.5/src/gmxlib/mshift.c, line: 102 Fatal error: Molecule in topology has atom numbers below and above natoms (575). You are probably trying to use a trajectory which does not match the first 575 atoms of the run input file. What I've done wrong and how I can define tpr file for trajectory made from several pdb files ? Thanks for help James -- gmx-users mailing listgmx-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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
[gmx-users] Covariance analysis of X-ray ensemble
Dear Gromacs users! I want to perform Covariance analysis of my x-ray data sets via g_covar -f trr.pdb -s x_ray.tpr -n index -o PCA_eigenval.xvg -v PCA_eigenvec.trr where trr.pdb is the trajectory made from the 30 x-ray structures (only c-alpha atoms were selected. How I could obtain x_ray.tpr file for such analysis? I've tried to use tpr from full atomic model of the same protein which I';ve simulated recently. For that p[rotein tpr file have been already created. From that model via make_ndx I've defined only backbone atoms corresponded to the atoms in my pdb ensemble. On the next step I've used tpbconv on protein.tpr with index file to make reduced tpr file with atoms corresponded to the backbone of the pdb-ensemble. Now when I run g_covar with my ensemble and reduced tpr file I obtain error *** glibc detected *** g_covar: malloc(): memory corruption: 0x7f27df53e018 *** On other hand if I specify for g_covar full-atomic tpr file with the index ( where atoms corresponded to the trr.pdb are mentioned) g_covar -f trr.pdb -s protein.tpr -n index -o PCA_eigenval.xvg -v PCA_eigenvec.trr I obtain another error Calculating the average structure ... Reading frame 0 time1.000 WARNING: number of atoms in tpx (575) and trajectory (575) do not match --- Program g_covar, VERSION 4.5.5 Source code file: /tmp/build/gromacs-4.5.5/src/gmxlib/mshift.c, line: 102 Fatal error: Molecule in topology has atom numbers below and above natoms (575). You are probably trying to use a trajectory which does not match the first 575 atoms of the run input file. What I've done wrong and how I can define tpr file for trajectory made from several pdb files ? Thanks for help James -- gmx-users mailing listgmx-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
Re: [gmx-users] Covariance analysis of X-ray ensemble
Hi James, You don't need a .tpr file. A .gro or .pdb file will do as well. Unless you insist on doing mass-weighted PCA. Cheers, Tsjerk On Fri, Jan 11, 2013 at 4:04 PM, James Starlight jmsstarli...@gmail.comwrote: Dear Gromacs users! I want to perform Covariance analysis of my x-ray data sets via g_covar -f trr.pdb -s x_ray.tpr -n index -o PCA_eigenval.xvg -v PCA_eigenvec.trr where trr.pdb is the trajectory made from the 30 x-ray structures (only c-alpha atoms were selected. How I could obtain x_ray.tpr file for such analysis? I've tried to use tpr from full atomic model of the same protein which I';ve simulated recently. For that p[rotein tpr file have been already created. From that model via make_ndx I've defined only backbone atoms corresponded to the atoms in my pdb ensemble. On the next step I've used tpbconv on protein.tpr with index file to make reduced tpr file with atoms corresponded to the backbone of the pdb-ensemble. Now when I run g_covar with my ensemble and reduced tpr file I obtain error *** glibc detected *** g_covar: malloc(): memory corruption: 0x7f27df53e018 *** On other hand if I specify for g_covar full-atomic tpr file with the index ( where atoms corresponded to the trr.pdb are mentioned) g_covar -f trr.pdb -s protein.tpr -n index -o PCA_eigenval.xvg -v PCA_eigenvec.trr I obtain another error Calculating the average structure ... Reading frame 0 time1.000 WARNING: number of atoms in tpx (575) and trajectory (575) do not match --- Program g_covar, VERSION 4.5.5 Source code file: /tmp/build/gromacs-4.5.5/src/gmxlib/mshift.c, line: 102 Fatal error: Molecule in topology has atom numbers below and above natoms (575). You are probably trying to use a trajectory which does not match the first 575 atoms of the run input file. What I've done wrong and how I can define tpr file for trajectory made from several pdb files ? Thanks for help James -- gmx-users mailing listgmx-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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing listgmx-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
Re: [gmx-users] Covariance analysis of X-ray ensemble
Tsjerk, thanks for suggestion! By the way I've found in the pca.log ( that time pca was done on trajectory as well as TRP ( not pdb) files as the inputs ): Read 30 frames from cam_xray_coors_bb.pdb (time 1 to 30 ps) Read reference structure for fit from x_ray.tpr Analysis group is 'System' (575 atoms) Fit group is 'System' (575 atoms) Analysis is non-mass weighted Fit is non-mass weighted Diagonalized the 1725x1725 covariance matrix Trace of the covariance matrix before diagonalizing: 350.847 Trace of the covariance matrix after diagonalizing: 350.847 Wrote 1725 eigenvalues to PCA_eigenval.xvg Wrote reference structure to PCA_eigenvec.trr Wrote average structure to PCA_average.pdb and PCA_eigenvec.trr Wrote eigenvectors 1 to 29 to PCA_eigenvec.trr It seems that cov.analysis was done also as non-mass weighted. Actualy I extract eigenvectors for further essential dynamics sampling runs. In the literature I've found that for EDA eigenvectors from only non-mass weighted PCA are suitable. So if its true in what cases mass weighted eigenvectors might be used? James 2013/1/11 Tsjerk Wassenaar tsje...@gmail.com: Hi James, You don't need a .tpr file. A .gro or .pdb file will do as well. Unless you insist on doing mass-weighted PCA. Cheers, Tsjerk On Fri, Jan 11, 2013 at 4:04 PM, James Starlight jmsstarli...@gmail.comwrote: Dear Gromacs users! I want to perform Covariance analysis of my x-ray data sets via g_covar -f trr.pdb -s x_ray.tpr -n index -o PCA_eigenval.xvg -v PCA_eigenvec.trr where trr.pdb is the trajectory made from the 30 x-ray structures (only c-alpha atoms were selected. How I could obtain x_ray.tpr file for such analysis? I've tried to use tpr from full atomic model of the same protein which I';ve simulated recently. For that p[rotein tpr file have been already created. From that model via make_ndx I've defined only backbone atoms corresponded to the atoms in my pdb ensemble. On the next step I've used tpbconv on protein.tpr with index file to make reduced tpr file with atoms corresponded to the backbone of the pdb-ensemble. Now when I run g_covar with my ensemble and reduced tpr file I obtain error *** glibc detected *** g_covar: malloc(): memory corruption: 0x7f27df53e018 *** On other hand if I specify for g_covar full-atomic tpr file with the index ( where atoms corresponded to the trr.pdb are mentioned) g_covar -f trr.pdb -s protein.tpr -n index -o PCA_eigenval.xvg -v PCA_eigenvec.trr I obtain another error Calculating the average structure ... Reading frame 0 time1.000 WARNING: number of atoms in tpx (575) and trajectory (575) do not match --- Program g_covar, VERSION 4.5.5 Source code file: /tmp/build/gromacs-4.5.5/src/gmxlib/mshift.c, line: 102 Fatal error: Molecule in topology has atom numbers below and above natoms (575). You are probably trying to use a trajectory which does not match the first 575 atoms of the run input file. What I've done wrong and how I can define tpr file for trajectory made from several pdb files ? Thanks for help James -- gmx-users mailing listgmx-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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
Re: [gmx-users] Covariance analysis of X-ray ensemble
Hi James, The default is non-mass weighted. If you want to relate the principal components to normal modes, and want to obtain mode frequencies, you (formally) need to include the masses. Cheers, Tsjerk On Fri, Jan 11, 2013 at 7:46 PM, James Starlight jmsstarli...@gmail.comwrote: Tsjerk, thanks for suggestion! By the way I've found in the pca.log ( that time pca was done on trajectory as well as TRP ( not pdb) files as the inputs ): Read 30 frames from cam_xray_coors_bb.pdb (time 1 to 30 ps) Read reference structure for fit from x_ray.tpr Analysis group is 'System' (575 atoms) Fit group is 'System' (575 atoms) Analysis is non-mass weighted Fit is non-mass weighted Diagonalized the 1725x1725 covariance matrix Trace of the covariance matrix before diagonalizing: 350.847 Trace of the covariance matrix after diagonalizing: 350.847 Wrote 1725 eigenvalues to PCA_eigenval.xvg Wrote reference structure to PCA_eigenvec.trr Wrote average structure to PCA_average.pdb and PCA_eigenvec.trr Wrote eigenvectors 1 to 29 to PCA_eigenvec.trr It seems that cov.analysis was done also as non-mass weighted. Actualy I extract eigenvectors for further essential dynamics sampling runs. In the literature I've found that for EDA eigenvectors from only non-mass weighted PCA are suitable. So if its true in what cases mass weighted eigenvectors might be used? James 2013/1/11 Tsjerk Wassenaar tsje...@gmail.com: Hi James, You don't need a .tpr file. A .gro or .pdb file will do as well. Unless you insist on doing mass-weighted PCA. Cheers, Tsjerk On Fri, Jan 11, 2013 at 4:04 PM, James Starlight jmsstarli...@gmail.com wrote: Dear Gromacs users! I want to perform Covariance analysis of my x-ray data sets via g_covar -f trr.pdb -s x_ray.tpr -n index -o PCA_eigenval.xvg -v PCA_eigenvec.trr where trr.pdb is the trajectory made from the 30 x-ray structures (only c-alpha atoms were selected. How I could obtain x_ray.tpr file for such analysis? I've tried to use tpr from full atomic model of the same protein which I';ve simulated recently. For that p[rotein tpr file have been already created. From that model via make_ndx I've defined only backbone atoms corresponded to the atoms in my pdb ensemble. On the next step I've used tpbconv on protein.tpr with index file to make reduced tpr file with atoms corresponded to the backbone of the pdb-ensemble. Now when I run g_covar with my ensemble and reduced tpr file I obtain error *** glibc detected *** g_covar: malloc(): memory corruption: 0x7f27df53e018 *** On other hand if I specify for g_covar full-atomic tpr file with the index ( where atoms corresponded to the trr.pdb are mentioned) g_covar -f trr.pdb -s protein.tpr -n index -o PCA_eigenval.xvg -v PCA_eigenvec.trr I obtain another error Calculating the average structure ... Reading frame 0 time1.000 WARNING: number of atoms in tpx (575) and trajectory (575) do not match --- Program g_covar, VERSION 4.5.5 Source code file: /tmp/build/gromacs-4.5.5/src/gmxlib/mshift.c, line: 102 Fatal error: Molecule in topology has atom numbers below and above natoms (575). You are probably trying to use a trajectory which does not match the first 575 atoms of the run input file. What I've done wrong and how I can define tpr file for trajectory made from several pdb files ? Thanks for help James -- gmx-users mailing listgmx-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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing
