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On 31/10/2011 10:19 PM, Steven Neumann wrote:
<blockquote
cite="mid:CAKZJqQGgNR0Xvfaof0XB0tBch4wi3TNfOTv-hJMrPnCDB+hqvg@mail.gmail.com"
type="cite">
<div>Dear Gmx Users,</div>
<div> </div>
<div>My system consists of 10 ligands and protein. I am
calculating the hydrogen bonds between each residue and my
ligands (LIG). The overall charge of each ligand is zero.</div>
<div>I used:</div>
<div> </div>
<div><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 9pt;
mso-fareast-font-family: 'Times New Roman'; mso-ansi-language:
EN-US; mso-fareast-language: EN-GB; mso-bidi-language: AR-SA"
lang="EN-US">g_hbond -f md2.trr -s md2.tpr -n SystemGRP.ndx
-num RESIDUEwithLigandsHbond.xvg</span></div>
<div><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 9pt;
mso-fareast-font-family: 'Times New Roman'; mso-ansi-language:
EN-US; mso-fareast-language: EN-GB; mso-bidi-language: AR-SA"
lang="EN-US"></span> </div>
<div><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 9pt;
mso-fareast-font-family: 'Times New Roman'; mso-ansi-language:
EN-US; mso-fareast-language: EN-GB; mso-bidi-language: AR-SA"
lang="EN-US">And I found one residue with avergae number of
hydrogen bonds = 2.2 per time frame which is quite a lot
comparing to other residues.</span></div>
<div><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 9pt;
mso-fareast-font-family: 'Times New Roman'; mso-ansi-language:
EN-US; mso-fareast-language: EN-GB; mso-bidi-language: AR-SA"
lang="EN-US"></span> </div>
<div><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 9pt;
mso-fareast-font-family: 'Times New Roman'; mso-ansi-language:
EN-US; mso-fareast-language: EN-GB; mso-bidi-language: AR-SA"
lang="EN-US">Then I calculated the nonbonded energy between
this residue and my 10 ligands:</span></div>
<div><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 9pt;
mso-fareast-font-family: 'Times New Roman'; mso-ansi-language:
EN-US; mso-fareast-language: EN-GB; mso-bidi-language: AR-SA"
lang="EN-US"></span> </div>
<div><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 9pt;
mso-fareast-font-family: 'Times New Roman'; mso-ansi-language:
EN-US; mso-fareast-language: EN-GB; mso-bidi-language: AR-SA"
lang="EN-US"><span style="FONT-FAMILY: 'Times New Roman';
FONT-SIZE: 12pt; mso-fareast-font-family: 'Times New Roman';
mso-ansi-language: EN-GB; mso-fareast-language: EN-GB;
mso-bidi-language: AR-SA">g_energy -f md2.edr -s topol.tpr
-o 127LJwithLIG.xvg - SR - LJ energy res127-LIG = 0.659
kcal/mol</span></span></div>
<div><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 9pt;
mso-fareast-font-family: 'Times New Roman'; mso-ansi-language:
EN-US; mso-fareast-language: EN-GB; mso-bidi-language: AR-SA"
lang="EN-US"><span style="FONT-FAMILY: 'Times New Roman';
FONT-SIZE: 12pt; mso-fareast-font-family: 'Times New Roman';
mso-ansi-language: EN-GB; mso-fareast-language: EN-GB;
mso-bidi-language: AR-SA"></span></span> </div>
<div><span style="font-family: 'Courier New'; font-size: 9pt;"
lang="EN-US"><span style="font-family: 'Times New Roman';
font-size: 12pt;">
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal">g_energy -f
md2.edr -s topol.tpr -o 127CoulombWithLIG.xvg -SR -
Coulomb res127-LIG = -32.579 kcal/mol</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"> </p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal">The total
energy (nonbonded) as a sum of LJ and Coulomb = -31.919
kcal/mol</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"> </p>
<p style="margin: 0cm 0cm 0pt;" class="MsoNormal">My
question is: how is it possible that contribution of
Coulombic attraction is so high if the overall charge of
each ligand is zero? </p>
</span></span></div>
</blockquote>
<br>
Consider two neutral dipoles fixed either parallel or anti-parallel
to each other.<br>
<br>
<blockquote
cite="mid:CAKZJqQGgNR0Xvfaof0XB0tBch4wi3TNfOTv-hJMrPnCDB+hqvg@mail.gmail.com"
type="cite">
<div><span style="font-family: 'Courier New'; font-size: 9pt;"
lang="EN-US"><span style="font-family: 'Times New Roman';
font-size: 12pt;">
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal">And why the
LJ potential seems to be slightly repulisve? Is the
evidence of hydrophobic attraction?</p>
</span></span></div>
</blockquote>
<br>
First, define "hydrophobic attraction" :-)<br>
<br>
Mark<br>
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