Re: [AMBER] question about dihedral angles

From: David A Case <>
Date: Tue, 1 Dec 2020 21:07:17 -0500

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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Received on Tue Dec 01 2020 - 18:30:03 PST
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