Hi
As the above mail mentioned,in order to calculates the RDF of all atoms in
residues 1 to 229 to all atoms in all residues named WAT. We used the input
file: radial rdf 0.05 12 :1-229 :WAT closet density
Here, the result graph shows two peaks at (1.8,500) and
(3,450),respectively. We what to know:
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?
2. What about the y-coordinate represents?
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?
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Received on Thu Sep 20 2012 - 00:30:02 PDT
