[gmx-users] Problems with g_anaeig

James Starlight jmsstarlight at gmail.com
Fri Jan 25 06:40:08 CET 2013


as I told previously to Justin ( lets to consider the problems with
g_anaeig only in that topic to avoid producing doubles ) the problem
is not in the average structure (it looks fine) but in the
filter.xtc trajectory produced by g_anaeig. When I load that xtc to
any structure in vmd I obtained dynamics picture of my protein with
broken geometry (its look loke my protein was shrunken). But when I
compared eigenvectors ( produced by g__covar) with the the results of
the same cov.analysis where there were no such problems in filter.xtc
I obtained full coverage in the same modes ( so g_covar in both cases
produce apropriate cov.matrix and the problem only in g_anaeig .


2013/1/25 Mark Abraham <mark.j.abraham at gmail.com>:
> On Tue, Jan 22, 2013 at 8:22 PM, James Starlight <jmsstarlight at gmail.com>wrote:
>> Dear Gromacs users!
>> There is some bug  with g_anaeig the souce of which I could not fully
>> understand.
> Good Advice: until you can almost write a code patch to fix it, be very
> hesitant in suggesting any software has a bug. The best people to help
> solve the issue are often those who wrote the code, and you don't want them
> annoyed with you :-)
>   I have problems when I perform PCA of X-ray data set.
>> Below you can my workflow.
>> g_covar -f b2ar_xray_coors.pdb  -s ref.pdb  -o PCA_eigenval.xvg -v
>> PCA_eigenvec.trr -av PCA_average.pdb -last 8
>> g_anaeig -v PCA_eigenvec.trr -s ref.pdb  -f b2ar_xray_coors.pdb -rmsf
>> eigrmsfPCA.xvg -filt
>> here b2ar_xray_coors.pdb  is the trajectory made from 10 X-ray
>> structures of my protein (only main chain atoms are included)
>> ref_pdb is the first frame of that trajectory
>> As the result I've obtained reasonable eigenvalues and aigenvectors
>> from g_covar BUT when I check filter trajectory ( produced by
>> g_anaeig) fitted it to the ref.pdb or to the averaged structure in
>> both cases I've obtained very distorted geometry of the  protein in
>> thefiltered trajectory. I have no such problems in case of PCA of MD
>> trajectory ( when  -f trajectory.trr is from the md snapshots not from
>> x-ray structures)
>> How it could be fixed ?
> How have you excluded the hypotheses that your reference structure is not a
> valid representative of the middle of the range of variation? Or even that
> the X-ray structural ensemble really is one?
> Mark
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