AMBER: ptraj hydrogen bonding defaults

From: Michael Lerner <>
Date: Fri, 17 Aug 2007 18:26:09 -0400


In the ptraj hbond section of the AMBER 8 manual (top of page 212), it says:

  "The default is no angle cutoff and a distance of 3.5 angstroms."

However, it looks like the actual defaults are 120 degrees and 3.0
Angstroms. I think the relevant lines are ptraj/actions.c 4726-4730:

        * distance and angle cutoff
    hbondInfo->distanceCutoff =
argumentStackKeyToFloat(argumentStackPointer, "distance", 3.0);
    hbondInfo->angleCutoff =
argumentStackKeyToFloat(argumentStackPointer, "angle", 120.0);

And the output files agree with that when you use the details. I don't
have AMBER 9 to check the source code, but the AMBER 9 manual also
says "the default is no angle cutoff and a distance of 3.5 angstroms"
(this time on page 263).

What are the default values supposed to be?



Biophysics Graduate Student
Carlson Lab, University of Michigan
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Received on Sun Aug 19 2007 - 06:07:45 PDT
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