AMBER Archive (2004)

Subject: Re: AMBER: Molecular Frame

From: Bill Ross (
Date: Fri Jan 02 2004 - 17:40:54 CST

> I want to calculate order parameter (S2) of backbone N-H.
> To calculate rotation correlation function of N-H bond vector,
> I need to calculate the bond vector respect to molecular frame.
> Is there any pre-set way or program to do this easily?

If you want to measure the angle of the bond vector with some
vector derived from the overall molecule, you will need to
define the latter vector. One possibility might be the line
drawn between centers of mass of two groups of atoms. Another
possibility might be to use the vector N-{molecule center of mass}
as the measurement vector. These two could be done with carnal
and possibly ptraj. Or you could take the angle of N-H with
respect to the principle axis of the molecule, which might
require some programming to accomplish. I am not familiar
with the mathematical definition of "molecular frame", so
am just throwing out some ideas.

In any case, it sounds like you are interested in per-snapshot
'internal' measurements, so superimposing snapshots may not be
relevant except to perform an approximate measurement whereby
the N-H vector of the positioned molecule could be used for
further calculations.

Bill Ross

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