Re: [AMBER] Hydrogen bond analysis

From: Daniel Roe <>
Date: Tue, 22 Jul 2014 09:13:35 -0600


The way that ptraj defines hydrogen bond 'acceptor' is in the sense of
electrons, which is why two masks are required for acceptor (one for heavy
atoms and one for hydrogen atoms).

I recommend that you look into using the 'hbond' command in cpptraj, which
is much simpler to use and has the ability to automatically search for
hydrogen bond donors and acceptors (be aware however that cpptraj defines
the hydrogen bond donor as the heavy atom bonded to the hydrogen which is
opposite the ptraj definition). A tutorial for the cpptraj hbond command is
currently in preparation. In the meantime, the Amber 14 manual has a lot of
information on the cpptraj 'hbond' command.

Hope this helps,


On Sat, Jul 19, 2014 at 4:56 AM, menwer momo <> wrote:

> Dear Amber users,
> In the tutorial3/section6, file analyse_hbond.ptraj
> I understood that one should exclude the N and C termini and any proline
> within the protein
> but I am not sure what does 20.N :2-20.H in the following line means.
> acceptor mask :2-11,13-16,20.N :2-20.H
> Many Thanks.
> _______________________________________________
> AMBER mailing list

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) 585-6208 (Fax)
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Received on Tue Jul 22 2014 - 08:30:02 PDT
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