Hi ros,
Thanks for your prompt reply.! I looked up the 'nastruct' in CPPTRAJ, and I
don't think the parameters are suitable for calculate DNA bend angle. Also,
I don't know how to use Curves+ and Canal. ='( By any chance, you know how
to use those software with AMBER trajectories? =)
Yew Mun
On Mon, Jan 6, 2014 at 10:46 PM, ros <rodrigogalindo.gmail.com> wrote:
> Hello!
>
> The program Curves+ and Canal (
> http://gbio-pbil.ibcp.fr/Curves_plus/Using_Curves+.html ) 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 ( http://x3dna.org/ )
>
> So, lots of options! Hope this helps.
>
> Rodrigo.
>
>
> On Mon, Jan 6, 2014 at 2:55 AM, Yip Yew Mun <yipy0005.gmail.com> 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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--
Regards
Yip Yew Mun
Graduate, Masters
Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University
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Received on Tue Jan 07 2014 - 00:30:03 PST
