actually there are more than 1 step to get this plot in pytraj.
I follow Dan's comment and just made an example for pytraj here
http://amber-md.github.io/pytraj/doc/build/html/tutorials/hbonds.html
Hai
On Mon, Aug 24, 2015 at 10:40 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> If I understand what you want to do, there is not currently a way to
> get this plot directly in cpptraj. What you would have to do is save
> the time series for each hydrogen bond with the 'series' keyword, then
> add up # of hydrogen bonds involving the same residue in an additional
> step. Alternatively you may be able to use pytraj, the python
> interface to cpptraj to do this in one step.
>
> Hope this helps,
>
> -Dan
>
>
>
> On Sun, Aug 23, 2015 at 10:15 PM, Garisekurthi Satheesh
> <gschembio.uohyd.ac.in> wrote:
> > Dear Amber Users,
> >
> > Some one please provide cpptraj command for plotting number of hydrogen
> > bonds with respect to residue number.
> >
> > Please kindly give your answer.
> >
> > Thank you.
> > GS
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>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Mon Aug 24 2015 - 10:30:05 PDT
