Re: [AMBER] Calculating B-factor in ptraj

From: Gonzalo Jimenez <>
Date: Tue, 10 Apr 2012 11:16:04 -0700

Dear Mish,

Maybe you can try to generate an average structure first and then re-run
ptraj again to rms your frames using that average pdb as reference. I'd bet
that you'll obtain better b-factors (it happened the same to me)
Good luck,,

From: "mish" <>
Sent: Tuesday, April 10, 2012 10:55 AM
To: "AMBER Mailing List" <>
Subject: [AMBER] Calculating B-factor in ptraj

> 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.
> Sincerely
> Mish
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Received on Tue Apr 10 2012 - 11:30:03 PDT
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