AMBER Archive (2004)

Subject: Re: AMBER: B factors from simulation and from cryst

From: Joseph Nachman (nachman_at_hera.med.utoronto.ca)
Date: Mon Jan 26 2004 - 15:23:49 CST

Hello Vlad -

Not necessarily - the B factors reflect to some extent the effect of
crytal packing forces, so unless you exactly reproduce theexact crystal
conditions (intermolecular contacts with symmetry mates), the simultae4de
B factors may be diferent from the crystallographic ones, at least in
regions involved in crystal packing intermolecular contacts.

Cheers,

Joseph

 On Mon, 26 Jan 2004, Vlad Cojocaru wrote:

> Dear Amber comunity,
> I have a question regarding the B factors:
> Should one expect the B factors calculated from the simulation to match
> exactly the B factors from the X-Ray structure? If not could somebody
> explain what to expect in general?
>
> In my case I a simulating a protein-rna complex and in general the B
> factors for the protein atoms calculated from the simulation are smaller
> comparing to the ones from the crystal structure except the N and C
> terminus where they are bigger? Would that be a concern for the
> simulation's quality?
> Thank you very much for any replies
> Best wishes
> vlad
>
> 

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Joseph Nachman				Department of Biochemistry
nachman_at_hera.med.utoronto.ca		University of Toronto
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tel: +1 416 978-5510			Toronto, Ontario M5S 1A8
fax: +1 416 978-8548			Canada
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