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: Thu Jan 19 2006 - 06:59:39 CST

be careful about interpreting RMSD as "stability".
it only means stable in the sense that the reference
structure is stable in the simulation. If the structure
moves to another structure and has low fluctuations
then it is "stable" in the new structure.

haixiao jin wrote:
> 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
> <mailto: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.
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu <mailto:amber_at_scripps.edu>
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> <mailto:majordomo_at_scripps.edu>
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu