Re: [AMBER] CPPTRAJ hydrogen bond analysis

From: Daniel Roe <>
Date: Tue, 4 Feb 2020 14:42:26 -0500


The 'hbond' command can be told to only analyze specific atoms via
several different masks; there is no need to strip out atoms

E.g. 'hbond .N,H,C,O' will only look for hydrogen bonds with atoms
named N, H, C, and O. See the manual for full details and examples.


On Tue, Feb 4, 2020 at 10:22 AM Rui Chen <> wrote:
> Hello,
> Good morning. When I perform H-bond analysis, do I need to remove the ions
> form the trajectories or just specify the backbone atoms to ignore the
> ions? Thank you.
> Best regards,
> Rui
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Received on Tue Feb 04 2020 - 12:00:02 PST
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