Re: [AMBER] calculating intramolecular hydrogen bonding

From: Daniel Roe <>
Date: Fri, 5 Oct 2012 11:43:11 -0600


On Fri, Oct 5, 2012 at 1:29 AM, Vijay Manickam Achari
<> wrote:
> I found one thread in amber mailing list talking about this ( but I am not so clear how the "angle turning off" (angle = -1.0) could give intramolecular hydrogen bonding values.

You don't need to turn off the angle calculation, that just removes
the angle criterion from hydrogen bond determination.

You could also try the 'hbond' command in cpptraj which doesn't
require you to specify donors/acceptors ahead of time.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Fri Oct 05 2012 - 11:00:03 PDT
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