[AMBER] diff. between avg/rep structures & connectivity problem in PDB files

From: vaibhav dixit <vaibhavadixit.gmail.com>
Date: Sun, 7 Oct 2012 14:54:02 +0530

Dear Amber community members,
What is the difference between the average and representative structures
generated during clustering MD trajectories.
If I guessed correctly, average structure means "average of all the
coordinates" in a given cluster. So the avg. structure *might not be
chemically meaningful* structure (for say RMSD analysis), as I experienced
while comparing and visualizing them. Please correct me if I'm wrong here.

So the question is:
while comparing structural aspects in each cluster and between different
clusters of different proteins, is it better/meaningful to use the
representative structure?
Because an average structure might have artifacts (e.g. in detail below).
How the representative structure is chosen by the clustering algorithm? No
information is given in the manual and the original paper.
pubs.acs.org/doi/abs/10.1021/ct700119m
How can I incorporate the avg. structure in my analysis?

Artifacts in the avg. structure:
I'm having problem visualizing average PDB files generated by the
clustering algorithm.
Unusual bonds are appearing (especially in the side chains) when I load
these file either in pymol or vmd. Check the TYR267 residue in the attached
file. Here distance between two meta carbons in the ring is 1.4 A as
opposed to 2.4 A in a normal TYR benzene ring, a strange observation?
Please let me know if I made a mistake in measuring the distances*. *This
is making comparison of side chain positions difficult among two PDB
structures.
Probably it is because, its an avg. of all coordinates. I guess the rules
set for bond prediction based on distance in pymol/vmd are leading to these
unusual bonds being seen.

I have checked the original MD trajectory, it appears normal?

Thank you.

-- 
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X,  S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in



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Received on Sun Oct 07 2012 - 02:30:03 PDT
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