Date: Mon, 25 Oct 2010 08:03:47 -0500
I am looking for a method to identify the positions of water molecules (what amino acids are closest to and hydrogen bonded to a given water molecule) in the x-ray structure of a protein and during dynamics simulations. I am interested in finding which water molecules are lost and which ones are gained during MD. I also want to determine instances in which intramolecular hydrogen bonds of the protein are lost and replaced by hydrogen bonds to water. Can someone suggest a way to do this?
John
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