Re: [AMBER] [cpptraj] Angle between atom and two centroids

From: David A Case <>
Date: Fri, 18 May 2018 08:04:34 -0400

On Fri, May 18, 2018, Eiros Zamora, Juan wrote:
> I’m interested in calculating the ‘bending' angle of a protein that has
> two globular domains joined by a flexible linker.
> I think I can do this by defining a centroid for each globular domain
> (the center of mass) and calculate the angle formed by these two
> centroids to an atom located in the linker that joins them.
> Can this be done in cpptraj? If so, could you point me towards the
> relevant commands?

Since you want to compute an angle, I'd suggest firing up cpptraj, and
typing "help angle":

> help angle
  [help angle]
        [<name>] <mask1> <mask2> <mask3> [out <filename>] [mass]
  Calculate the angle between atoms in masks 1-3.

Here mask1 would identify the atoms in the first domain, mask2 the atom
in the linker, and mask3 the atoms in the second domain.

There is an example on p, 629 of the Amber 2018 Reference Manual.

...good luck...dac

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Received on Fri May 18 2018 - 05:30:03 PDT
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