Re: [AMBER] H-bond analysis

From: Daniel Roe <>
Date: Wed, 8 Nov 2017 11:31:32 -0500


On Wed, Nov 8, 2017 at 7:17 AM, Mustafa Alhaji Isa
<> wrote:
> PTRAJ: hbond all out hbond.agr :19, 88, 128.C,O,N,H time 20.00

To use this form of the 'hbond' command (determining donors/acceptors
automatically from atom mask) you'll need to use cpptraj. Cpptraj is
freely available with AmberTools or from a GitHub repository:

Also, either remove the spaces from your atom mask expression or
enclose the expression in quotes.


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 Wed Nov 08 2017 - 09:00:02 PST
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