Re: [AMBER] CPPTRAJ printout auto-detected hbond donor/acceptor

From: Daniel Roe <>
Date: Fri, 6 Nov 2020 08:53:37 -0500


On Fri, Nov 6, 2020 at 4:25 AM Gustaf Olsson <> wrote:
> I was curious regarding the definition of hbond donors/acceptors in cpptraj. From what I understand, cpptraj allows a relatively loose definition of these and is capable of of some degree of auto-detection.

As stated in the manual, a hydrogen bond in the hbond command 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 (default 3 Ang) and the A-H-D angle is greater
than the angle cutoff (default 135 deg.) a hydrogen bond is considered
formed. Both cutoffs can be adjusted by the user.

> If my understanding is correct, is it possible to run cpptraj in a way, potentially just using the prmtop/inpcrd files, to print out all identified donors/acceptors?

You can do this by setting the actions debug level to something
greater than 1 (so put e.g. 'debug actions 1' before the 'hbond'
command) and running on 1 frame. Maybe that should be a keyword


> Best regards
> // Gustaf
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Received on Fri Nov 06 2020 - 06:00:04 PST
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