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

James Starlight jmsstarlight at gmail.com
Fri Jan 11 16:04:30 CET 2013

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
*** 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

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


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