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<div class="gmail_quote">On Wed, Aug 31, 2011 at 3:44 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br><br>Steven Neumann wrote:<br>
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<div class="h5"><br><br>On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br><br><br> Steven Neumann wrote:<br><br> Hi Gromacs Users,<br> I have calculated hydrogen bonds and collisions between my<br> ligands and every single residue using g_hbond. Looking at the<br> criteria adpoted by Gromacs I found impossible that number of<br>
hydrogen bonds were higher than number of collisions... And what<br> is interesting in one of my residue I obtained result like<br> this... All Hbonds with Glycine - 1872, All Collisions 704.<br> Does anyone know how is it possible?<br>
<br><br> I don't know how any of your numbers are possible (1872 H-bonds<br> forming with a glycine?), or what you are defining as a collision<br> and how you calculated it. Please provide the exact commands that<br>
you're using. If you're equating a contact (e.g. from g_mindist)<br> with a collision, then realize that the default criteria for a<br> contact are very different than the geometric criteria for a<br> hydrogen bond.<br>
<br> -Justin<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></div></div> jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> <<a href="http://vt.edu/" target="_blank">http://vt.edu/</a>> | <a href="tel:%28540%29%20231-9080" target="_blank" value="+15402319080">(540) 231-9080</a><br>
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<br><br> My system is made of 10 ligands and one protein. I used command:<br> g_hbond -f md.trr -s md.tpr -n res91.ndx -num 91with10LIGbonds.xvg<br> 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.<br>
</div></blockquote><br>I forgot to mention in the previous message that there is no value in summing the hydrogen bonds over time. Some of those H-bonds may be distinct, and others may be the same H-bond that has broken and subsequently re-formed. I doubt anyone would find real value in saying that 10 ligands formed 1872 H-bonds with glycine over a trajectory.<br>
<font color="#888888"><br>-Justin</font>
<div class="im"><br></div></blockquote>
<div>Obviosuly, but it can provide you some information about binding affinity - some ligands remains close to some residues longer than the others so by sum of this values you can assess residues with higher binding affinity.</div>
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<div>Steven</div>
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<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">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? Steven<br>
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<div class="h5">-- <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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