[AMBER] Define angle between planes of monomers in a hexamer

From: Rosellen, Martin via AMBER <amber.ambermd.org>
Date: Thu, 29 Sep 2022 13:28:52 +0000

Hi all,

I want to investigate the dynamics of monomers in a hexamer. Therefore, I would like to define a plane (or two vectors) for each monomer and calculate the angles of neighbouring monomer planes. I had a look at the ‘vector’ function where I can define a vector from centres of mass atom mask1 to atom mask2, which is not optimal in my case.

‘vector corrplane’ seems to be related since its description goes like this: “corrplane: This defines a vector perpendicular to the (least-squares best) plane through the atoms in <mask1>.”

What I actually want from this is the "(least-squares best) plane through the atoms in <mask1>”. In theory, I could rotate that vector back to be parallel with the plane again and define second vector by rotating this vector 90 degrees in the plane. I hope there is an easier solution.

Is there a way to get the plane from “vector corrplane"?

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Received on Thu Sep 29 2022 - 06:30:02 PDT
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