Re: [AMBER] Percent occupancy of a hydrogen bond

From: Jason Swails <>
Date: Thu, 7 Aug 2014 11:32:05 -0400

On Thu, Aug 7, 2014 at 8:00 AM, menwer momo <> wrote:

> Hi,
> In a protein-DNA complex, a certain hydrogen bond between two amino acids
> has 3.4 angstrom distance between acceptor and donor atoms.
> Hydrogen bond analysis shows that the occupancy of this bond during
> production runs is 30%, does this reflect that the bond is not stable?
> ​​

Or is it possible that t
> ​​
> he reason of this low percent occupancy is conformational change in the
> side chains of the two amino acids throu
> ​​
> gh production runs, and does not necessarily mean that this bond is not
> stable in reality?

​The _only_ information it gives is that the hydrogen bond exists only 3
out of every structures in your ensemble.​ If you want an explanation as
to _why_ they hydrogen bond breaks, you will need to do further analysis.
 Both of your explanations seem reasonable, but based on just the hbond
analysis it is entirely speculation.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Aug 07 2014 - 09:00:02 PDT
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