<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
<title></title>
</head>
<body text="#000000" bgcolor="#ffffff">
On 7/11/2010 8:02 PM, leila karami wrote:
<blockquote
cite="mid:AANLkTi=FfGMNhTaFrggE2-8gbFuWVsaig49e7MkVbDB5@mail.gmail.com"
type="cite">
<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>
</blockquote>
<br>
Take a look at section 7.4 of the manual, where it groups the tools
by analysis type, and use that to see which tools might be useful.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTi=FfGMNhTaFrggE2-8gbFuWVsaig49e7MkVbDB5@mail.gmail.com"
type="cite">
<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
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group</pre>
<br>
</blockquote>
<br>
</body>
</html>