Re: [AMBER] Calculating the bending angle of a DNA sequence

From: ros <>
Date: Mon, 6 Jan 2014 07:46:29 -0700


The program Curves+ and Canal ( ) will give you the
total bend for a single frame or for a series of frames (please notice that
it will not work with NetCDF trajectories, so you have to use plain text
traj files) Also, CPPTRAJ has a command called 'nastruct' that will give
you information about helical inclination, tip, twist, etc. Similar
information can be obtained using the 3DNA tool ( )

So, lots of options! Hope this helps.


On Mon, Jan 6, 2014 at 2:55 AM, Yip Yew Mun <> wrote:

> Hi, I'm currently simulating a protein-DNA complex. I wish to ask if there
> are any tools in Amber that would allow me to calculate the bending angle
> of the DNA for a trajectory. Thanks.
> Sent from my iPad
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Received on Mon Jan 06 2014 - 07:00:03 PST
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