Re: [AMBER] Cpptraj hbond criteria

From: Daniel Roe <>
Date: Tue, 5 Oct 2021 08:43:48 -0400


On Wed, Sep 22, 2021 at 2:04 PM Veenis, Andrew Jay <> wrote:
> So, it seems that a hydrogen bond is considered to be formed when the A-D distance is <= (not <) and the A-H-D angle is >= (not >). Is this correct?

Yes, the code is the ultimate arbiter of what is being done so you are
correct. I'll update the manual.

I'm guessing that what happened here is that once upon a time the
criteria in the code were distance < cut and angle > acut, but over
the course of many a code refactor the code changed and the manual was
sadly left behind. As you note, it should make no practical difference
for almost all calculations. Best to be consistent though.

Thanks for the report.


> While this makes no real practical difference in the results of an analysis, it’s helpful to know the true definition for documenting purposes.
> Thanks,
> Drew
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Tue Oct 05 2021 - 06:00:03 PDT
Custom Search