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, [UTF-8] "Mag. rer. nat. Hannes Wallnöfer" 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 didn´t find anything like that in the manual.
>
> Thanks,
> Hannes Wallnöfer
> University of Innsbruck
>
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  = Department of Chemistry      -                              =
  = University of Rochester      -                              =
  = Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) =
  = http://www.pas.rochester.edu/~yildirim/                     =
  ---------------------------------------------------------------

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