Re: [AMBER] standard deviation of Hbond lengths and angles

From: Daniel Roe <>
Date: Mon, 7 Dec 2015 09:04:07 -0700


On Sun, Dec 6, 2015 at 8:20 AM, Hadeer ELHabashy
<> wrote:
> Is it possible to calculate the standard deviation of the Hydrogen bonding
> 's lengths and angles directly using the Hbond command ?!

It's certainly possible, but currently not straightforward. This data
is currently not stored by the 'hbond' command. What you would
currently have to do is save the hydrogen bond time series data (using
the "series" keyword), read that data back in, then use a combination
of the 'filter' command with the 'hbond' series data followed by the
'distance'/'angle' commands to calculate the raw distance and angle
values when the hydrogen bond is present, and lastly calculate your
average/stdev from those values (using e.g. the 'avg' analysis
command). The problem is you would have to do this for *each* hydrogen
bond separately, which is going to be pretty slow.

This is certainly something I can consider adding to cpptraj 'hbond'
output at some point.


PS - If you have any programming experience, it may be easier to e.g.
modify the HbondType structure in Action_Hbond.cpp to hold the sum of
squared distances/angles for the purpose of calculating the standard
deviation yourself.

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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
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Dec 07 2015 - 08:30:03 PST
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