AMBER Archive (2006)

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

From: haixiao jin (jinhx952_at_gmail.com)
Date: Wed Jan 18 2006 - 22:58:28 CST

thank you, carlos.
yes, your reply is reasonable. but i still have something confused and need
your help.
you see, the RMSD of simulation A is lower than that of simulation B. in
my opinion, the protein in simulation A is more stable than that in
simulation B. are you agree with me?
however, the result of B-factor of two simulation seems that the protein in
simulation A is more flexible than that of simulation B. so, it seems that
it not consistant in the two results. i am confused. is there anything
wrong? thank you!

On 1/19/06, Carlos Simmerling <carlos_at_ilion.bio.sunysb.edu> wrote:
>
>
>
> 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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