Dear Erik thanks for your time and consideration.
you said by multiplying the existence functions for hbonds between protein and water and the hbonds between water and DNA, then using Justin's script, I can obtain percentage each water medited hydrogen bond during trajectory. and also you said I need to create a corresponding index file too. now I write steps. please check accuracy of them. 1) obtaining hbond.ndx and hbmap.xpm from g_hbond tool for hbonds between protein and water. 2) obtaining hbond.ndx and hbmap.xpm from g_hbond tool for hbonds between dna and water. 3) multiplying the existence functions how to multiply these two existence functions? how to make new index file? should I write those lines from two hbond.ndx file above in which particular water hbonds to both protein and DNA? -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group
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