Hi,
Part of this question was answered previously,
http://archive.ambermd.org/201209/0323.html - hopefully you are
getting these replies.
On Thu, Sep 20, 2012 at 3:01 AM, Yanyan MENG <mengyanyan21.gmail.com> wrote:
> 1. Can I take the meaning of this result as that a hydration layer would
> appear around each protein atom in a 1.8Å distance? Or any other meanings?
The first hydration layer would appear to be more within 3.4 ang since
1.8 ang corresponds to the water hydrogen atoms only. Remember, these
are distances from solute atoms and not from the solute surface.
> 2. What about the y-coordinate represents?
The RDF is essentially a normalized histogram, see the AmberTools
manual (cpptraj:radial) for more details.
> 3.One more puzzle, could you explain us what the 0.05 in the input files
> means? And what the bases to set this parameter?
This information is also in the manual - it is the bin spacing for the
histogram used to construct the RDF.
Hope this helps.
-Dan
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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
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Received on Thu Sep 20 2012 - 09:00:02 PDT
