AMBER Archive (2004)

Subject: Re: AMBER: A question about RMSD calculation

From: David A. Case (case_at_scripps.edu)
Date: Tue Mar 02 2004 - 13:52:05 CST

On Tue, Mar 02, 2004, yonchen wrote:
>
> I got a result about RMSD which I could not understand.
>
> First I calculated the RMSD of the first two residue in a protein
> seperately. Then I calculated the RMSD of them together. According to my
> understanding of RMSD definition, the value of latter should be between
> the first two values since it was the avarage of them. However the
> result is that the value of latter is bigger than both of them.

What you got is what you should have expected. It is generally
easier to fit any single residue to a template than it is to fit
simultaneously two residues. The result for two residues is _not_ the average
of the results for one.

This is hard to explain in words...you probably just have to do the math....

...dac

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