[AMBER] question about dihedral angles

From: Gordon Richard Chalmers <gordoncs.uga.edu>
Date: Tue, 1 Dec 2020 23:43:50 +0000

I have a quick question as to how AmberTools20, tleap,
or cpptraj rotates the molecule about a phi or psi dihedral

If the residue i is of interest then these angles are specified
by the 4-sequential atoms, which I calculate.

%% phi C(i-1)-N-CA-C
%% psi N-CA-C-N(i+1)

However, in creating a new pdb file are these residues < i
rotated in the case of phi and >i in the case of psi? And the O
and H of residue i the phi and psi rotation.

-- I can't find the documentation for dihedral angle rotations in
the Amber manual, unfortunately, and I want to reproduce these
rotations as tleap or cpptraj does. I lot of the comments about
dihedral angle rotations are buried in the pages. My chi angle
rotations work well.

This is a good picture of these angles,

Dihedral angle - Wikipedia<https://en.wikipedia.org/wiki/Dihedral_angle#/media/File:Protein_backbone_PhiPsiOmega_drawing.svg>
A dihedral angle is the angle between two intersecting planes. In chemistry, it is the angle between planes through two sets of three atoms, having two atoms in common.In solid geometry, it is defined as the union of a line and two half-planes that have this line as a common edge.In higher dimensions, a dihedral angle represents the angle between two hyperplanes.

I do write a lot of my own code, and would be willing to use tleap or cpptraj,
if this is documented.

Thank you, Gordon
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Received on Tue Dec 01 2020 - 16:00:02 PST
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