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<div class="gmail_quote">On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
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<div class="h5"><br><br>Steven Neumann wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi Gromacs Users,<br> I have calculated hydrogen bonds and collisions between my ligands and every single residue using g_hbond. Looking at the criteria adpoted by Gromacs I found impossible that number of hydrogen bonds were higher than number of collisions... And what is interesting in one of my residue I obtained result like this... All Hbonds with Glycine - 1872, All Collisions 704.<br>
Does anyone know how is it possible?<br> <br></blockquote><br></div></div>I don't know how any of your numbers are possible (1872 H-bonds forming with a glycine?), or what you are defining as a collision and how you calculated it. Please provide the exact commands that you're using. If you're equating a contact (e.g. from g_mindist) with a collision, then realize that the default criteria for a contact are very different than the geometric criteria for a hydrogen bond.<br>
<br>-Justin<br><br>-- <br>==============================<u></u>==========<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" target="_blank" value="+15402319080">(540) 231-9080</a><br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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<div>My system is made of 10 ligands and one protein. I used command:</div>
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<div><span style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman'; mso-ansi-language: EN-GB; mso-fareast-font-family: 'Times New Roman'; mso-fareast-language: EN-GB; mso-bidi-language: AR-SA">g_hbond -f md.trr -s md.tpr -n res91.ndx -num 91with10LIGbonds.xvg</span></div>
<div><span style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman'; mso-ansi-language: EN-GB; mso-fareast-font-family: 'Times New Roman'; mso-fareast-language: EN-GB; mso-bidi-language: AR-SA"></span> </div>
<div><span style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman'; mso-ansi-language: EN-GB; mso-fareast-font-family: 'Times New Roman'; mso-fareast-language: EN-GB; mso-bidi-language: AR-SA">Where I specified in the index file two groups: 10 ligands and Glycine residue. So I have calculated hbonds (second column) and collisions (third column) and then I made a sum of all frames during 100 ns simualtion time (one frame every 50 ps) obtaining 1872 hbonds and 703 collisions between Glycine and 10 ligands. I did it with every residue to assess binding affinity of different amino acids. </span></div>
<div><span style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman'; mso-ansi-language: EN-GB; mso-fareast-font-family: 'Times New Roman'; mso-fareast-language: EN-GB; mso-bidi-language: AR-SA">Criteria for collision is distance <3.5 A, and fo hbond distance <3.5 A and angle. So when calcualting hbond and collisions the number of hbonds has has to be smaller while collision takes into account hbonds as welll. I obtained results like this for all other residues which seems to be correct. Am I right? </span></div>
<div><span style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman'; mso-ansi-language: EN-GB; mso-fareast-font-family: 'Times New Roman'; mso-fareast-language: EN-GB; mso-bidi-language: AR-SA"></span> </div>
<div><span style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman'; mso-ansi-language: EN-GB; mso-fareast-font-family: 'Times New Roman'; mso-fareast-language: EN-GB; mso-bidi-language: AR-SA">Steven</span></div>