[gmx-users] Covariance analysis of X-ray ensemble

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Jan 11 16:21:12 CET 2013

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.



On Fri, Jan 11, 2013 at 4:04 PM, James Starlight <jmsstarlight at 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
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4

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