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

From: Gustaf Olsson <>
Date: Mon, 9 Nov 2020 08:40:53 +0000

Setting the debug level > 1 did produce a promising start:

HBOND: Searching for Hbond donors/acceptors in region specified by *
        Distance cutoff = 3.000, Angle Cutoff = 135.000

The printout from running the analysis with no additional input produces a list of "Acceptor-only atoms” and "Donor/acceptor sites”. This is roughly what I was looking for. I can solve this with some awk/grep combination though what I was hoping for was the same output on a “per resname” basis. My test system had 100 carboxylic acid molecules and water. I get 100 entries for the "carbonyl oxygen" and another 100 for the “hydroxyl group”. I was hoping to get entries on a “residue name/type” basis “on XXX found these acceptors/donors, on YYY, on ZZZ”.

Don’t know if this is of any greater interest to anyone else and should most likely not be considered a priority issue.

Thank you for you reply and suggestion
Best regards
// Gustaf

> On 6 Nov 2020, at 14:53, Daniel Roe <> wrote:
> Hi,
> 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
> option...
> -Dan
>> Best regards
>> // Gustaf
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Received on Mon Nov 09 2020 - 01:00:02 PST
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