Re: Measuring rigid-body rotation with AMBER

From: Bill Ross <>
Date: Fri 26 Jan 2001 13:33:25 -0800 (PST)

        I was wondering if anyone knew of a neat way to measure the
        rotation of a whole group of atoms with respect to a reference
        set. I have a modular protein, where if you superimpose one
        domain with the reference, another domain is rotated as a rigid
        body compared to the reference set. How can I get a numerical
        value for this rotation using the AMBER suite of programs (advice
        on any other programs that would do the same would also be

Using carnal you could measure torsion between points formed
by centers of mass. Comparing this measurement on the two
sets would give you what you want, provided it's possible
to choose appropriate atoms or groups of atoms to measure on.

Bill Ross
Received on Fri Jan 26 2001 - 13:33:25 PST
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