Re: [AMBER] hbond in Ambertools

From: Daniel Roe <>
Date: Thu, 5 Sep 2013 08:20:21 -0600


On Thu, Sep 5, 2013 at 1:31 AM, Neha Gandhi <> wrote:
> hbond donormask :11.N :11.H acceptormask :9.O3P,9.O2P,9.O1P :9.H out GlyNH-t1p.out avgout GlyNH-t1pavg.dat

Note that this syntax is cpptraj-only, and there are a couple of
problems with it as you have it. For 'donormask' you only need to
specify a single mask corresponding to donor heavy atoms, e.g.
'donormask :11.N'. You can specify an additional mask for donor
hydrogen atoms with 'donorhmask' but that is unnecessary in this case.
Similarly, for 'acceptormask' you only need a single mask
corresponding to acceptor atoms (and the mask you have specified is
malformed); it should read 'acceptormask :9.O3P,O2P,O1P', or
alternatively 'acceptormask :9.O?P'.

Let me know if that helps,


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 Thu Sep 05 2013 - 07:30:03 PDT
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