AMBER Archive (2007)

Subject: AMBER: ptraj hydrogen bonding defaults

From: Michael Lerner (mlerner_at_umich.edu)
Date: Fri Aug 17 2007 - 17:26:09 CDT

Hi,

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?

Thanks,

-michael 

-- 
Biophysics Graduate Student
Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner
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