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: >> 0x00007f27df53e018 *** >> >> >> 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 time 1.000 >> 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 list gmx-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 list gmx-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 list gmx-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