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

[Lucio Ricardo Montero Valenzuela]

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 <tsjerkw at 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 <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
> > Canada
> > --
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