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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

[https://upload.wikimedia.org/wikipedia/commons/thumb/3/3c/Dihedral_angle.svg/1200px-Dihedral_angle.svg.png]<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

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

[https://upload.wikimedia.org/wikipedia/commons/thumb/3/3c/Dihedral_angle.svg/1200px-Dihedral_angle.svg.png]<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

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