AMBER Archive (2006)

Subject: Re: AMBER: ptraj hbond analysis troubles

From: Robert Duke (
Date: Thu Oct 05 2006 - 20:55:42 CDT

Thanks Tom, I clearly was half befuddled when trying to get the angle stuff
straight here. I also did an (angle - 180) instead of an (180 - angle) in
there somewhere. Geez. - Bob

----- Original Message -----
From: "Thomas Cheatham" <>
To: <>
Sent: Thursday, October 05, 2006 3:43 PM
Subject: Re: AMBER: ptraj hbond analysis troubles

>> Okay, I had my donors and acceptors backward here, thinking of "H donor"
>> instead of "electron pair donor to the H bond". So indeed you can get
>> the generic designations to work, and pick up reasonable other H bonding
> Yes, this is "my bad" as the saying goes.
>> On angles, Tom clarified for me that the cutoff angle is indeed the
>> value below which the donor--H--acceptor is not permitted to go, so
>> specifying angle 120.0 (the default) excludes bonds where this angle is
>> 0-60 degrees. Here's the confusing point. In the printout, such bond
>> angles would be reported as angles in the range of 60-180 degrees (so
>> the angle in the series printout has had 180 subtracted from the actual
>> donor--H--acceptor angle, and 0 here is a nice linear H bond. Tom does
> Actually, I think the opposite. For the hbond angle cutoff, a value of
> 120 means that the hbond angle has to be greater than 120,
> donor -- H -----
> ( \ ) angle2
> angle1 acceptor
> 180.0 is a linear hydrogen bond. In practice I either use no cutoff for
> the angle (angle -1.0) or something liberal like 90.0. The cutoff angle
> is angle1 in that figure above.
> For some reason I cannot remember, I report the angle as
> (180. - angle) or angle2 in the figure.
> So, for an angle cutoff of 120, the reported angles will be 0-60.
> Who knows how my convoluted mind was working when I dreamed this up as a
> research prototype that we eventually released. Clearly work is necessary
> to improve the manual, to show tutorials, to auto-detect lists of
> donors/acceptors, to store histograms of the distances, etc.
> Sorry for the further confusion.
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to