AMBER Archive (2006)

Subject: Re: AMBER: is there any relationship between RMSD and B-factor?

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Wed Jan 18 2006 - 21:53:26 CST

haixiao jin wrote:
>
> Dear Amber users,
>
> Two MD simulation were performed for a complex to test the
> importance of a key conserved residues. there is the result of RMSD
> and B-factor I obtained. The RMSD of simulation A is lower than that
> of simulation B, while the B-factor of simultiaon A is larger than
> that of simulation B. is it reasonable? Is there any relationship
> between RMSD and B-factor?
>
>
No. RMSD is distance from a particular structure. B-factors relate to
fluctuations
about an average structure. That average could be close or far from the
structure
that you compare to for RMSD.
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