Hi,
the B-Factor is not the mean square displacement, which is often called
<u^2>. B is defined as:
B= 8 pi^2 <u^2>
Therefore a B-factor of 20 means ca. 0.5 A positional uncertainty (in a
perfect structure. The actual relation for real X-ray cryst. is a bit more
complicated). Unfortunately, I have no citation for that (other than my
Ph.D. thesis which you are welcome to cite ;-) ).
Kind Regards,
Thomas
On Sat, September 25, 2010 12:15 am, Ashutosh Shandilya wrote:
> I am sending this mail again even a little idea would guide me.
> I have seen RCSB structures where theres a B factor value ranging from
> 20-60.I dont know the unit but someone suggested thst it is Armstrong
> square
> but what does these high value imply.(because if we take the square root
> its
> still 4-9 Angstrom).Does the crystal structure coordinates are so
> uncertain.
>
> When I run MD simulation while heating and equilibrating there is change
> of
> 1.5-2 Angstrom in RMSD.IS that fine even if I run on crystal structure
> there
> is change and in that course the ligand moloecule loses some of the
> interaction and I get slightly lesser binding affinity due to the lateral
> shift of ligand molecule and the protein.Also sometimes it is proposed
> that
> we should dock the ligand after running a small simulation.
>
> On emore thing if I do homology modeling with 70% similarity i get a
> structure of 0.3 Angstrom from the crystal structure but when I run the
> simulation while heating and equilibrating the structure I get has 2
> Angstrom from the crystal structure.
>
> So is this normal or shall I change the protocol for better understanding
> and please guide me bit more about the application of B factor.What are
> the
> other things that I can analyze with the MD simulation data besides
> energy,RMSD, inter atomic distances,B factor etc.
> I am eagerly waiting for the replies.
>
> Thanks in advance.
>
> Regards
> Shandilya Ashutosh
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>
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Fri Sep 24 2010 - 22:00:03 PDT
