Re: [AMBER] Regarding cut-off distance in hydrogen bond

From: Daniel Roe <>
Date: Mon, 29 Jul 2019 09:11:41 -0400


This is explained in the cpptraj 'hbond' command section of the Amber manual:

"[dist <dcut>] Distance cutoff for hydrogen bonds (acceptor to donor
heavy atom, default 3.0 Å)."

"A hydrogen bond is defined as being between an acceptor heavy atom A,
a donor hydrogen atom H, and a donor heavy atom D. If the A to D
distance is less than the distance cutoff and the A-H-D angle is
greater than the angle cutoff a hydrogen bond is considered formed."

Hope this helps,


On Sun, Jul 28, 2019 at 10:32 AM richa anand <> wrote:
> Dear friends,
> I want to know which atoms (heavy atoms or h-atoms) are use to define
> cut-off distance to calculate hydrogen-bonds through CPPTRAJ or PTRAJ.
> Thanking You,
> Richa
> IIIT-Allahabad
> _______________________________________________
> AMBER mailing list

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Received on Mon Jul 29 2019 - 06:30:04 PDT
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