AMBER Archive (2006)

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

From: Andy Purkiss (a.purkiss_at_mail.cryst.bbk.ac.uk)
Date: Thu Jan 19 2006 - 07:19:06 CST

Dear haixiao,

The B-factor is a single number generated from the fluctuations of the
atoms in all the frames, whereas the rmsd only compares two structures.

If you want to properly compare the rmsd of the structures with the
B-factors, you need to calculate the rmsd of each set of coordinates of
the trajectory and look at their mean and standard deviation.

Is your second figure the rmsd between the start and end structures? Or
is it the mean of the rmsd for all the frames used to calculate the
B-factor? If the first, then you should calculate the mean and standard
deviation of the whole rmsd during the whole simulation and see if the
two sets of data overlap.

I also think that the differences are small. A 0.4-0.5Angstrom
difference in RMS for the residues is not likely to be very significant.

Don't forget that flexibility and stability are not the same thing in a
protein. Many protein have flexible loops, but are stable overall.

Andy

On Thu, 2006-01-19 at 12:58 +0800, 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> 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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-- 
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