[gmx-users] kind of contacts in protein-dna interaction during simulation

[leila karami]

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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