AMBER Archive (2004)

Subject: Re: AMBER: A question about RMSD calculation

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Mar 02 2004 - 13:53:11 CST

> 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. Is this
> result possible?

Did you try for best-fit in all 3 cases? If so this could explain it.

Bill
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