On 28/08/2012 4:09 PM, James Starlight wrote:
Mark,
Thanks for explanation!
2012/8/27, Mark Abraham <[email protected]>:
Did you construct a correlation matrix from side chain atoms?
Yes, and there is some degree of correlation between adjacent side
chains but lack of any cooperativety between distant side-chains. In
comparison in that protein there were alot of cooperativity in motion
of the distinct backbones.
Then that might be the conclusion, but that's your judgement to make
from the full context. It's hardly likely that there'd be magical
"action at a distance," but motion along the lines of Newton's cradle
could have been detected and would be fascinating to see in a protein
(e.g. http://www.youtube.com/watch?v=H7P4xOUPYVw). Motion exactly like
Newton's cradle does require cross-correlation to observe, because of
the intrinsic asynchronicity, but that would require particular
plasticity conditions.
I suppose that it might be due to the
relatively limited degree of freedom of the backbones (2 dihedrals
with 3 minimum conformations) in comparison to the side-chains so the
correlation in the backbone might be more expected.
Backbone atoms can only move in concert with others, yes.
In addition as I've told you during analysis of filtered.xtc processed
trajectory I didnt observe any fluctuations of side chains on the
whole.
Yes, but the amplitude of single-side-chain motions is necessarily
small, so it doesn't follow that you should observe it in the
eigenvectors with the largest fluctuations. There's no direct connection
to the energy required for such motions, either. You should be looking
at some small peptide systems to learn how to make observations of
motion you know occurs, before trying to observe hypothesized motion.
Finally I've noticed some bugs in the visualistion of the
side-chains of the structures processed after g_covar ( e.g
EDA_average.pdb) In that case the geometry of some side-chains (mainly
of aromatic rings) were very distorted. Why this might occur ?
http://www.gromacs.org/Documentation/Terminology/Average_Structure
Mark
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