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 <[email protected]>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 [email protected] > 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 [email protected]. > * 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 [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
