AMBER Archive (2006)

Subject: Re: AMBER: angle between two vectors

From: David A. Case (
Date: Thu Oct 12 2006 - 13:14:14 CDT

On Thu, Oct 12, 2006, Lwin, ThuZar wrote:

> Do you have any suggestion on how to do the following using amber
> ptraj?
> Vector 1: Assign a vector between atom A and B.
> Vector 2: Assign another vector between atom C and D.
> Then calculate angle between vector 1 and vector 2.

My best guess is to use the vector command to write out files with the two
vectors as a function of time, then use a short awk or perl script to compute
the angles.

(This would be a good functionality to have inside ptraj, but as far as I
know, it is not there now.)


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