Re: [AMBER] question about dihedral angles

From: Gordon Richard Chalmers <>
Date: Wed, 2 Dec 2020 04:36:39 +0000

I am going to write this again because the note wasn't
read. The atoms are specified for the rotations.

TLeAP or Cpptraj should be documented in this if we are
supposed to do molecular work using Amber. This topic
is a little basic in protein work and should be documented
in Amber.

Also, each 4 atom pair defining 2 planes specify different
angular rotations and should commute. This means the order
of the phi/psi rotations in the residues is independent and

Gordon Chalmers

From: David A Case <>
Sent: Tuesday, December 1, 2020 9:07 PM
To: AMBER Mailing List <>
Subject: Re: [AMBER] question about dihedral angles


On Tue, Dec 01, 2020, Gordon Richard Chalmers wrote:
>I have a quick question as to how AmberTools20, tleap,
>or cpptraj rotates the molecule about a phi or psi dihedral

The world's experts on this subject are right in your backyard: check
with Rob Woods or Lachele Foley, who probably have the longest
institutional memory about this.

The basic problem is that just saying you want to rotate about an angle
is not enough information. One also needs to specify which atoms (i.e.
which "side" of the torsion) should be moved. But the tleap syntax
doesn't include this, and it can be rather difficult to understand its
internal procedures for making this decision.

I'm less familiar with cpptraj handles this problem.


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