Re: [AMBER] Regarding impropers from and guessing from bond topology

From: Jason Swails <>
Date: Mon, 20 Oct 2014 00:27:52 -0400

> On Oct 20, 2014, at 12:16 AM, Arun Srikanth <> wrote:
> Thanks i will keep point [1] in mind.
> Two questions
> In amber,
> 1. If I have a dihedral let's say I-J-K-L. How is phi calculated in the
> dihedral potential expression. Is it the angle between the planes
> containing
> I-J-K and J-K-L

Yes. More precisely, it is the angle between the normal vectors of those two planes (which is easy to compute via cross products of the two vectors).

> 2. How is phi defined for an improper I-J-K-L with K as the central atom

Same way.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Sun Oct 19 2014 - 21:30:03 PDT
Custom Search