Re: [AMBER] hydrogen bond occupancy plot cpptraj

From: Daniel Roe <>
Date: Mon, 1 Aug 2016 11:23:57 -0600

If you want hydrogen bond occupancy vs time you can create the data
using the 'series' and 'uuseries'/'uvseries' keywords of the 'hbond'
command, e.g. for solute-solute hydrogen bonds:

hbond HB series uuseries HB.UU.gnu

Note that this syntax is for version 16 or greater.

If you want to plot the percent occupied for each hydrogen bond you
can extract the data from 'avgout'/'solvout' and plot using your
favorite graphing program.


On Sat, Jul 30, 2016 at 4:15 PM, Saman Yousuf ali
<> wrote:
> Dear all,
> Can anyone tell me how to plot hydrogen bond occupancy plot using cpptraj? Thanks in advance.
> Best Regards,Saman Yousuf Ali
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Aug 01 2016 - 10:30:02 PDT
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