Hi Ashutosh,
I guess, the B factor is unitless quantity. The B factor is temperature
dependent factor. The B-factor (or temperature factor) is an indicator of
thermal motion about an atom. However, it should be pointed out that the
B-factor is a mix of real thermal displacement, static disorder (multiple
but defined conformations) and dynamic disorder (no defined conformation),
and all the overlap between these definitions.
A low B-factor meaning that the position of the atom has been determined
with accuracy. Typically B-factors of Alpha Carbons (CA) are lower than
atoms located at side chain extremities.
For the rcsb pdb file the value ranges from 1-100. But for the MD run the
value is much larger (upto 200 in your case). So I think you are getting the
correct value for your analysis.
Hirdesh
On Tue, Sep 14, 2010 at 11:22 AM, Ashutosh Shandilya
<izerokelvin.gmail.com>wrote:
> Hi to all
> I used this script to calculate the Bfactor.The temprature factor variation
> was quite large (20-400).I want to know what is the unit of Bfactor in this
> case and the values I am getting is that right if the units is Angstrom.
>
> trajin complex_equi.mdcrd
> center origin
> reference complex_wat.crd
> atomicfluct out bfac.dat byres .CA bfactor
>
>
> Thanks
> Shandilya Ashutosh
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Received on Mon Sep 13 2010 - 23:30:03 PDT
