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
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= University of Rochester - =
= Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) =
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Received on Sun Dec 02 2007 - 06:07:39 PST
