AMBER Archive (2009)

Subject: Re: [AMBER] B-factor

From: Cristina Sisu (csds2_at_cam.ac.uk)
Date: Sat Oct 17 2009 - 05:58:34 CDT

Thank you TEC3, now all is clear!

On 16 Oct 2009, at 23:16, Thomas Cheatham III wrote:

>
>> I know that lots has already been discussed about the b-factor, but
>> I've
>> noticed some strange behaviour when calculating the b-factor with
>> ptraj.
>> If I ask to calculate just the bfactor without calculating previously
>> the rms I obtain some very strange/huge values for the b-factor. 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 b-factor is calculated as 8/3*p^2*fluct, but aren't the two
>> actions done independently?
>
> Yes, B-factor is independent of RMS fit, i.e. it does not implicitly
> do an
> RMS fit... --tec3
>

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