Dear Oliver very thanks for your help.
Justin's perl script is good for direct hydrogen bonds, while I want to study water mediated hydrogen bonds and residence time and occupation of them. Are youe sure g_hbond give you residence time of hydrogen bonds? before you said you used a script to change the pdb file for compatibility with amber. please share me that. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group
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