<div>Dear Gmx Users,</div>
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<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>
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<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; 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">
<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? And why the LJ potential seems to be slightly repulisve? Is the evidence of hydrophobic attraction?</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"> </p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal">Thank you in advance,</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"> </p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal">Steven</p></span></span></div>