Thanks Pratul
The GitHub pages were useful. I want to begin by coding to read the data
out of the NetCDF trajectory (which is not straightforward unlike reading
from .crd) and analyse the extracted data. Was stuck at the first step
itself (reading data). But the links shared on this thread will definitely
help.
On Tue, Dec 11, 2018 at 6:04 PM Pratul Agarwal <pratul.agarwal-lab.org>
wrote:
> The GitHub pages for cpptraj and pytraj has some documentation for
> developers that may be relevant. If not, could you say a little more about
> what you are trying to do?
>
> Pratul K. Agarwal, Ph.D.
> (Editorial Board Member: PLoS ONE, Microbial Cell Factories)
> Web: http://www.agarwal-lab.org/
>
>
>
>
> On 12/11/2018 7:22 AM, Debostuti Ghoshdastidar wrote:
>
> Thanks for the response Pratul. I wanted to learn a bit on how to do it
> myself, so I cant write some analyses codes that may not be available in
> cpptraj (or pytraj).
>
> On Tue, Dec 11, 2018 at 5:48 PM Pratul Agarwal <pratul.agarwal-lab.org
> ><mailto:pratul.agarwal-lab.org>
> wrote:
>
>
>
> You can use cpptraj (installed in $AMBERHOME/bin during installation) for
> extracting frames and performing a wide range of analysis. The ability to
> read NetCDF trajectories is inbuilt into cpptraj.
>
> If you prefer python based program or functionality, pytraj is also
> available with similar functionalities. See documentation in AMBER manual
> (or a web search for pytraj will take you its documentation/home page).
>
> Pratul K. Agarwal, Ph.D.
> (Editorial Board Member: PLoS ONE, Microbial Cell Factories)
> Web: http://www.agarwal-lab.org/
>
>
>
>
> On 12/11/2018 2:16 AM, Debostuti Ghoshdastidar wrote:
>
> Dear Amber Users
>
> I was looking for some heads up on where I can start learning a bit about
> how to use python to work on Amber-generated NetCDF trajectory (extract
> data and analyse data from NetCDF trajectories).
>
> Any suggestions would be greatly appreciated.
>
> Thank you
>
>
>
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>
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>
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--
Debostuti Ghosh Dastidar
DST SERB National Post-Doctoral Fellow
Molecular Biophysics Unit
Indian Institute of Science, Bangalore
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Received on Tue Dec 11 2018 - 22:30:03 PST
