[AMBER] Calculating B-factor in ptraj

From: mish <smncbr.gmail.com>
Date: Tue, 10 Apr 2012 19:55:28 +0200

Dear all,

I am trying to calculate B-Factor of C-apha atoms by post processing
AMBER trajectories in ptraj. When I compute atomic fluctuation ( >
 atomicfluct out atomfluct_CA.out .CA byres ) values varies between 18 to
30 (which seems to me quite high) where as B-factor (> atomicfluct out
atomfluct_CA.out .CA byres bfactor) for same trajectories and same atom (
C-alpha) varies between 10000 to 25000; which is quite high. Values of
B-factors looks quite true because according to manual B-factor calculated
by multiplying the squared fluctuations by (8/3)pi**2.

I also tried to image the trajectories ( center :1-200 mass origin ; image
center familiar com :1-200) before calculating atomic fluctuation but the
fluctuations remains the same. Do you think I am doing some mistake in
commands (mentioned above) because If I align all the trajectories in vmd I
not see such a huge structural changed or movement of backbone atoms.

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Received on Tue Apr 10 2012 - 11:00:05 PDT
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