Re: [AMBER] calculating intramolecular hydrogen bonding

From: Vijay Manickam Achari <>
Date: Mon, 15 Oct 2012 09:19:08 +0100 (BST)

Dear Daniel,

Thanks for your reply.

As you suggested I have made the angle to be zero (angle 0.0) and run the ptraj program (in amber 12)  to get the intra-molecular hydrogen bonding (hydrogen bonding within the same residue). I checked the result of this calculation, which is in the form of table, looking for a line which should contain same residue numbers but unfortunately I could not find one. Means this command do not calculate the INTRA molecular hydrogen bonding.

Just curious to know, is there any other way to calculate this INTRA molecular hydrogen bonding?

Many thanks in advance.


Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,

 From: Daniel Roe <>
To: Vijay Manickam Achari <>; AMBER Mailing List <>
Sent: Saturday, 6 October 2012, 1:43
Subject: Re: [AMBER] calculating intramolecular hydrogen bonding

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 Mon Oct 15 2012 - 01:30:05 PDT
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