Dear Justin thanks for your attention.
1) my system consists of protein, dna, and water. In my .ndx file, protein-H is all of non hydrogen atoms of protein and dna. it is my nomination for .ndx file. 2) I want to obtain number of water molecule which are simultaneously closer than 3 A° from protein and DNA* *and not protein or dna.* * * * -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group
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