On 1/24/13 9:44 AM, James Starlight wrote:
Justin,
thanks. I've not known that posres were defined in the tpr file as well.
Sure, how else would mdrun know what to do? :)
By the way could you make your suggestion in my another topic which
I've posted some days ago about problem with the g_anaeig ( below I
coppy that issue).
If I had any insight into that issue, I would have posted before. Let's not
pollute threads with unrelated stuff, but it doesn't sound like a bug to me at
all; average structures need not have any physical significance.
-Justin
There is some bug with g_anaeig the souce of which I could not fully
understand. 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 ?
2013/1/24 Justin Lemkul <jalem...@vt.edu>:
On 1/24/13 7:21 AM, James Starlight wrote:
Dear Gromacs Users!
In the gromacs-4.6 version I have some problems with the trp files
obtained after reduction of atom subset via
tpbconv -f initial.tpr -n index -o reduced.tpr
where in index file reduced atom sub set was defined ( e.g c-alpha
atoms from the protein only )
then I'm using g_Covar to calculate covariance matrix from my
trajectory also with reduced atom subset and obtain error
g_covar -f xz.xtc -s reduced.tpr -o EDA_eigenval.xvg -v
EDA_eigenvec.trr -av EDA_average.pdb -tu ps
Program g_covar, VERSION 4.6
Source code file:
/home/own/Documents/distr/gromacs-4.6/src/gmxlib/mtop_util.c, line:
932
Software inconsistency error:
Position restraint coordinates are missing
the same error was obtained with other commands wich also require tpr
file as the input
How it could be filed?
Create a .tpr file that doesn't use position restraints.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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