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From: Prem <isodna05.gmail.com>

Date: Tue, 4 Dec 2007 15:59:29 -0600

Dear Hannes,

I dont know if u already got the scripts from Yildirim.

1. You can always write a script to calculate the cross product

between 2 vector in the same plane. ( make sure you do the right cross

product AxB vs BxA)

2. calculate this in each plane

3. find the angle between the two perpedicular vectors using dot product.

4. depending on your requirements you might either need theta or 180-theta.

good luck

prem

On 12/3/07, "Mag. rer. nat. Hannes Wallnöfer"

<hannes.wallnoefer.uibk.ac.at> wrote:

*> Dear Yildirim,
*

*>
*

*> thats exactly what i want to do, but i don´t need the average angle, but
*

*> the distribution of the anlge values over the simulation. It would be
*

*> great if you could help to get this.
*

*>
*

*> Best regards,
*

*> Hannes
*

*>
*

*>
*

*> Ilyas Yildirim schrieb:
*

*> > 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 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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*

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*

*> >> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
*

*> >>
*

*> >>
*

*> >>
*

*> >
*

*> >
*

*>
*

*> -----------------------------------------------------------------------
*

*> The AMBER Mail Reflector
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Received on Wed Dec 05 2007 - 06:07:32 PST

Date: Tue, 4 Dec 2007 15:59:29 -0600

Dear Hannes,

I dont know if u already got the scripts from Yildirim.

1. You can always write a script to calculate the cross product

between 2 vector in the same plane. ( make sure you do the right cross

product AxB vs BxA)

2. calculate this in each plane

3. find the angle between the two perpedicular vectors using dot product.

4. depending on your requirements you might either need theta or 180-theta.

good luck

prem

On 12/3/07, "Mag. rer. nat. Hannes Wallnöfer"

<hannes.wallnoefer.uibk.ac.at> wrote:

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Received on Wed Dec 05 2007 - 06:07:32 PST

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