Dear Justin thanks for your attention
with chang of hbond.ndx file my problem was solved. I have another question about g_hbond: if I want to obtain same information (percentage of existence of each hbond during my trajectory) about water mediated hydrogen bonds between protein and dna, for obtaining of hbond.ndx and hbmap.xpm files from g_hbond tool, what groups should be select? in previous state (protein-dna direct hydrogen bond), I selected 1) protein and 2) dna. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group
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