AMBER Archive (2005)

Subject: Re: AMBER: about the %occupied of hydrogen bond

From: Carlos Simmerling (carlos.simmerling_at_stonybrook.edu)
Date: Fri Sep 16 2005 - 09:49:04 CDT

maybe the original question is how to determine the % of time these two
GROUPS
are hydrogen bonded, and ptraj gives the % for the specific atom pairs.

For example, if the two atom pairs are H-bonded 50% each, it could be that
50% of the time there is a bifurcated Hbond and 50% no Hbond, or
it could be that It is 1 Hbond in 50% and the other in 50%, so 100%
of the time there is an Hbond between the groups. There just isn't a way
to tell that from the average data, you'll need to do some processing of
the
Hbonds vs time and see how often you have at least 1 of them.

If this isn't what you meant, please try to clarify exactly what you
want to calculate.

Thomas E. Cheatham, III wrote:

>>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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