Re: AMBER: about the %occupied of hydrogen bond

From: Thomas E. Cheatham, III <>
Date: Fri, 16 Sep 2005 08:30:58 -0600 (Mountain Daylight Time)

> I have gotten the hydrogen bond occupied. But in the followed two example, I
> don't know how to express the %occupied.
> atom
> residue
> distance
> %occupied
> WAT471-O(H1)
> ASP220 (OD2)
> 2.697
> 55.20

>From the information given, it is not clear where you obtained the data
shown, but if this was the hydrogen bond facility of ptraj, you in the
above observed an average distance (when formed, i.e. < cutoff) of 2.697
angstroms and an occupancy of 55.2% (meaning that it was formed slightly
more than half the time). Occupancies and average distances will depend
on the definition of the h-bond (cutoff distance, angle). If the distance
cutoff is longer, the occupancy may be higher.

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Received on Fri Sep 16 2005 - 15:53:02 PDT
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