AMBER Archive (2007)Subject: Re: AMBER: angle between vectors
From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Fri Nov 30 2007  11:28:59 CST
Dear Hannes,
I once did a similar analysis for a system; analyzing the angle between 2
different planes. I am not sure if amber has a script to calculate the
angle, but I wrote a script to do that. What it does is, it calculates the
vectors that are perpendicular to these planes, and takes the dot product
of these 2 vectors to calculate the angle. For each .mdcrd frame, it
calculates the angles and finds the average angle. Do you want to do a
similar analysis?
Best,
On Fri, 30 Nov 2007, [UTF8] "Mag. rer. nat. Hannes WallnÃ¶fer" wrote:
> Dear Amber users,
>
> i want to analyze the postion of two aromatic rings in my trajectory of
> a proteine MD simulation. I was able to define vectors perpendicular to
> the ring planes. Is there a possibility to calculate the angle between
> these two vectors? I didnÂ´t find anything like that in the manual.
>
> Thanks,
> Hannes WallnÃ¶fer
> University of Innsbruck
>
> 
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>

Ilyas Yildirim

= Department of Chemistry  =
= University of Rochester  =
= Rochester, NY 146270216  Ph.:(585) 275 67 66 (Office) =
= http://www.pas.rochester.edu/~yildirim/ =


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