AMBER Archive (2006)

Subject: Re: AMBER: angle between planes

From: Chris Moth (
Date: Fri Apr 07 2006 - 16:19:26 CDT

This is low tech - but.....

Wth ptraj you could certainly strip out all atoms but the 6 of interest,
trajout these out to a file, and then, with a bit of manipulation,
import them into,say, Excel for final calculation of angles between
planes (which will be calculation of angle between vectors normal to

I hope someone suggests something a bit more elegant...


John wrote:
> Dear All,
> I would like to calculate the relative orientation between side chains of
> opposite peptide strands. I believe that this can be done by defining a
> plane for each side chain using 3 carbon atoms from each side chain and then
> calculating the angle between the two planes by stepping through the
> trajectory frames. Is it possible to do something like this with ptraj? The
> "angle" function if I understand correctly calculates angles between 3 atoms
> and I donít think it would give a meaningful result for my problem.
> Thank you very much for any advice.
> Regards,
> John

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