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

From: Carlos Simmerling <>
Date: Wed, 18 Jan 2006 22:53:26 -0500

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
about an average structure. That average could be close or far from the
that you compare to for RMSD.
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Received on Thu Jan 19 2006 - 06:10:07 PST
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