AMBER Archive (2009)Subject: Re: [AMBER] Bfactor
From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Fri Oct 16 2009  17:16:35 CDT
> I know that lots has already been discussed about the bfactor, but I've
> noticed some strange behaviour when calculating the bfactor with ptraj.
> If I ask to calculate just the bfactor without calculating previously
> the rms I obtain some very strange/huge values for the bfactor. More
Yes! If you do not do the RMS fit, then you're atomic fluctuations will
include rotation and translation too and hence be large (although since
you are centering, you have removed much of the translation)... Ideally,
you would create an average structure over your trajectory, RMS fit to
this, and then do the "atomicfluct". You can RMS fit to first, but this
is not exactly the same as RMS fitting to the average structure.
> The two answers are completely different. I am not sure why is so. I
> know that bfactor is calculated as 8/3*p^2*fluct, but aren't the two
> actions done independently?
Yes, Bfactor is independent of RMS fit, i.e. it does not implicitly do an
RMS fit... tec3
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