Re: [AMBER] Hydrogen Bond

From: Daniel Roe <>
Date: Tue, 10 Oct 2017 15:16:35 -0400


You can do (b) and (c) with the 'hbond' command from cpptraj: see the
manual for details. Also see tutorial C5 here:

(a) can also be done, but only in a specific manner (i.e. you will get
details of *every* single solvent-solvent hydrogen bond in your
system) via the 'acceptormask' and 'donormask' keywords. Be aware this
will produce a ton of data.

Hope this helps,


On Mon, Oct 9, 2017 at 7:54 AM, ATUL KUMAR <> wrote:
> I have 3 component system which consists of water, co-solute(each co-solute
> molecule has 3 OH group) and protein. I am interested in calculating total
> number between
> (a) solvent-solvent. in this case water-water,
> (b) co-solute - solvent, where co-solute is hydrogen bond donor(since it
> has 3 -OH groups) and oxygen of water as hydrogen bond acceptor
> (c) co-solute - solvent, where co-solute is hydrogen bond donor and water
> as hydrogen bond acceptor.
> Thank you
> *Atul Kuamr jaiswal*
> Research Scholar
> School of Computational and Integrative Sciences
> Centre for Computational Biology and Bioinformatics (CCBB)
> JNU,New Delhi
> India.
> _______________________________________________
> AMBER mailing list

Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Tue Oct 10 2017 - 12:30:02 PDT
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