AMBER Archive (2003)

Subject: Re: helix movement

From: Bimo Ario Tejo (bimo7_at_linuxmail.org)
Date: Tue Jun 10 2003 - 06:19:05 CDT

Thanks Dr. Yuguang,

Unfortunately, my output trajectory is coordinates file, not velocity. Is it another way to observe the helix/domain movement quantitatively without velocity information? FYI, the helix creates a flap over the protein which is open and closed during catalysis.

Best wishes,

Bimo
ITB - Stutgart

----- Original Message -----
From: Yuguang Mu <ygmu_at_theochem.uni-frankfurt.de>
Date: Tue, 10 Jun 2003 12:47:42 +0200 (MEST)
To: Bimo Ario Tejo <bimo7_at_linuxmail.org>
Subject: Re: helix movement

> My rough idea is following :
> get coordinates and velocities of the helix/domain
> then calculate the exectly the overall translational and rotational
> velocities. then you may have a idea of such movement.
>
> Dr. Yuguang Mu
> Institute for Physical and Theoretical Chemistry
> J.W. Goethe University Frankfurt am Main
> Marie Curie Str. 11
> 60439 Frankfurt/Main, Germany
> Tel: +49-(0)69-798-29711
>
> On Tue, 10 Jun 2003, Bimo Ario Tejo wrote:
>
> > Dear Amber users,
> >
> > Does anyone have a tool to calculate the movement of helix and/or domain from Amber trajectory file? Superimposing some snapshots is useful, but it is not a quantitative way to describe such a movement.
> >
> > Any help is highly appreciated.
> >
> > Best regards,
> > Bimo
> > ITB - Stuttgart
> > --
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