# Re: [AMBER] question about dihedral angles

From: Gordon Richard Chalmers <gordoncs.uga.edu>
Date: Tue, 1 Dec 2020 23:49:46 +0000

To know, I calculate the phi and psi angles from a downloaded
pdb, have created a linear backbone peptide model of the protein,
and then rotate about the 4 atom axis (e.g. N-CA or CA-C) and
don't get the same angles as the initial pdb.

Am I correct that all residues have to be rotated before or after
the i'th residue and its axis defined by the 2 middle atoms and the
angle from the 4 atoms?

-----------------------

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

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,

https://en.wikipedia.org/wiki/Dihedral_angle#/media/File:Protein_backbone_PhiPsiOmega_drawing.svg
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.
en.wikipedia.org

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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Dec 01 2020 - 16:00:02 PST
Custom Search