AMBER Archive (2004)

Subject: AMBER: A question about RMSD calculation

From: yonchen (yonchen_at_ic.sunysb.edu)
Date: Tue Mar 02 2004 - 13:05:13 CST

Dear Amber users,

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. Is this
result possible?

Thanks a lot for the help.

Best wishes,
Yongzhi Chen

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