Re: [AMBER] hbond Backbone CPPTRAJ.

From: Daniel Roe <>
Date: Mon, 30 Jan 2017 11:53:15 -0500


On Sun, Jan 29, 2017 at 11:19 AM, Saman Yousuf ali
<> wrote:
> Dear All,I want to track only solute-solute backbone hydrogen bonds. If my protein residues are from 1-200 and ligand number is 201 (name LIG) then how to modify following script to calculate hydrogen bonds between protein-ligand.
> hbond Backbone :1-12.C,O,N,H avgout BB.avg.dat series uuseries bbhbond.gnu

Just modify your mask selection to include the ligand and add the
'nointramol keyword:

hbond Backbone :1-12.C,O,N,H|:201 nointramol ...

Hope this helps,


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 Mon Jan 30 2017 - 09:00:06 PST
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