AMBER Archive (2004)

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

From: Dr. Yong Duan (
Date: Mon Jan 26 2004 - 12:37:29 CST

In theory, yes, one should expect good agreement between the two. In
reality, qualitative agreement is more likely. Here are some factors that
may complicate the comparison.

1) Time scale. The typical ns (or so) simulations limit the conformations
sampled. The calculated B-factors are usually smaller than X-ray
2) Crystal packing. Unless the simulation was in the environment that
closely mimicks the crystalline environment, including concentration,
salt, buffer, and more importantly, in the same crystal lattice, one
should expect a bit difference. These typically make the surface residues
(particularly those in loops) a bit more mobile in the simulations.
3) Global translation and rotation. The calculated B-factors are usually
done after removal of global translation and rotation. In crystal, they
are accounted.
Other than these, force field errors can also make a bit difference.

Hope this helps.


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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