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.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
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