thanks for giving the insight about B factor but from where can I get your
PhD thesis so that I could have better idea.
regards
Shandilya Ashutosh
On 25 September 2010 10:08, <steinbrt.rci.rutgers.edu> wrote:
> 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 - 22:00:05 PDT
