<p class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: justify;"><span style="font-family: "Times New Roman","serif";">Hi gromacs users</span></p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: justify;"><span style="font-family: "Times New Roman","serif";"> </span></p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: justify;"><span style="font-family: "Times New Roman","serif";">In following article, in table 2, author brings <span style="color: rgb(35, 31, 32);">Protein–DNA contacts observed in the simulation.</span> </span></p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: justify;"><span style="font-family: "Times New Roman","serif";">I want to know how to obtain 1) <span style="color: rgb(35, 31, 32);">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 <span style=""> </span>Interfacial hydration water molecules were identified
by applying a cut-off 2.6 A <span style=""> </span>for the
distance of water to protein and DNA atoms simultaneously.</span></span></p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: justify;"><span style="font-family: "Times New Roman","serif"; color: rgb(35, 31, 32);"> </span></p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-family: "Times New Roman","serif"; color: rgb(35, 31, 32);">J. Mol. Recognit. 2004;
17: 120–131</span></p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: justify;"><span style="font-family: "Times New Roman","serif"; color: rgb(35, 31, 32);">DOI:10.1002/jmr.658</span></p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: justify;"><span style="font-family: "Times New Roman","serif"; color: rgb(35, 31, 32);"> </span></p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-family: "Times New Roman","serif"; color: rgb(35, 31, 32);">The role of
flexibility and hydration on the sequence-specific DNA recognition by the Tn916
integrase protein: a molecular dynamics analysis. </span></p>
<br clear="all"><br>-- <br><pre style="font-family: arial,helvetica,sans-serif;">Leila Karami<br>Ph.D. student of Physical Chemistry<br>K.N. Toosi University of Technology<br>Theoretical Physical Chemistry Group</pre><br>