Dear Amber users and developers
I'm now trying to calculate RDF in terms Wat,
preparing the ptraj input as shown below.
trajin protein-wat.mdcrd
radial RDF_H-vs-O 0.1 75 :WAT
However, I found an anomalous peak around 1[A],
This would be due to intra-molecular bonds betwenn H and O of water molecules.
Then, I would like to know how to ignore such intramolecular bonds
when I calculate RDF of water by using ptraj command, "radial".
Yours sincerely,
Ikuo KURISAKI
PS
I use AmberTools12 here.
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Received on Mon Jul 01 2013 - 03:00:02 PDT
