Hi gromacs users
In following article, in table 2, author brings Protein–DNA contacts observed in the simulation. I want to know how to obtain 1) Van der Waals interactions 2) percentage of population regarding Direct hydrogen bond, Van der Waals and Water-mediated hydrogen bond. In method section, Protein and DNA atoms were considered hydrogen-bonded if the distance between hydrogen and acceptor atoms was less than 2.6 A and the donor–hydrogen–acceptor angle was greater than 120. Hydrophobic interaction was defined when the distance between a pair of carbon atoms was less than 4 A Interfacial hydration water molecules were identified by applying a cut-off 2.6 A for the distance of water to protein and DNA atoms simultaneously. J. Mol. Recognit. 2004; 17: 120–131 DOI:10.1002/jmr.658 The role of flexibility and hydration on the sequence-specific DNA recognition by the Tn916 integrase protein: a molecular dynamics analysis. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group
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