AMBER Archive (2007)

Subject: Re: AMBER: ptraj hydrogen bonding defaults

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Fri Aug 17 2007 - 21:33:55 CDT

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

If in doubt, trust the code; you can always override the defaults by
choosing what you want...

-- tec3 at utah

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