Dear Justin very thanks for your reply.
I used for script two times: 1) between proten and interfacial waters. 2) between dna and same water molecules. using what I said above, can I obtain what water molecules form water-mediated hydrogen bond between protein and dna? if my way is wrong, please guide me about that. any suggestion will highly appreciated. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group
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