<br><br>
<div class="gmail_quote">On Wed, Aug 31, 2011 at 5:54 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">
<div class="im"><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">One question.... for Glycine it is easy to assess 3 possible hbonds which can create as hydrogen is only one atom as a side chain.<br>
How about other amino acids and their maximum hbonds they can create?<br> <br></blockquote><br></div>Any OH or NH group is a donor, any lone pair is an acceptor (though obviously not modeled explicitly in MD). The ability of MD force fields to agree with reality in this respect is debatable, but should come close.<br>
<br>-Justin<br></blockquote>
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<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Thank you Justin. Can you please clarify me something and tell me whether I am wrong. This is what I obtained from calulating hbonds between 10 ligands and Glycine. Each ligand serve 8 OH group (flavanoid) :</blockquote>
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<div><em><strong>Reading file md.tpr, VERSION 4.5.4 (single precision)<br>Specify 2 groups to analyze:<br>Group 0 ( r_96) has 7 elements</strong> -</em> this is my Glycine - 7 atoms (side chain - Hydrogen)<br>
<em><strong>Group 1 ( LIG) has 510 elements</strong> -</em> these are 10 ligands, 51 atoms each, 8 OH group<br><em><strong>Select a group: 0 1<br>Selected 0: 'r_96'<br>Select a group: Selected 1: 'LIG'<br>
Checking for overlap in atoms between r_96 and LIG<br>Calculating hydrogen bonds between r_96 (7 atoms) and LIG (510 atoms)<br>Found 81 donors and 112 acceptors </strong></em></div>
<div><strong><em></em></strong> </div>
<div><em>81 donors? It should be 80 when I have 10 ligands with 8 Oh group... Am I right?</em></div>
<div><em>112 acceptors? 7 atoms of my Glycine x 12 possibilities?</em></div>
<div><strong><em></em></strong> </div>
<div><em><strong>trn version: GMX_trn_file (single precision)<br>Reading frame 0 time 0.000<br>Will do grid-seach on 11x11x11 grid, rcut=0.35<br>Last frame 2000 time 100000.000<br>Average number of hbonds per timeframe 0.642 out of 4536 possible - </strong>that is understood = (112x81)/2</em></div>
<div><em></em> </div>
<div><em>So how many possibilities has Glycine in order to create hbond? Shall I choose just a side chain which is hydrogen?</em></div>
<div><em></em> </div>
<div><em>Steven</em></div>
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<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Steven
<div class="im"><br><br>On Wed, Aug 31, 2011 at 4:25 PM, Steven Neumann <<a href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a> <mailto:<a href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a>><u></u>> wrote:<br>
<br> Thank you for clarification Justin!!! The Manual is not as clear as<br> you :P<br> Steven<br><br> On Wed, Aug 31, 2011 at 4:00 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br>
</div>
<div class="im"> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br><br><br><br> Steven Neumann wrote:<br><br><br><br> On Wed, Aug 31, 2011 at 3:38 PM, Justin A. Lemkul<br>
<<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>><br></div>
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<div class="h5"> <mailto:<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><br><br> On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul<br> <<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>><br>
<mailto:<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>>><br> <mailto:<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>><br>
<mailto:<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<br> collisions between my<br> ligands and every single residue using<br> g_hbond. Looking<br>
at the<br> criteria adpoted by Gromacs I found impossible<br> that number of<br> hydrogen bonds were higher than number of<br> collisions...<br>
And what<br> is interesting in one of my residue I obtained<br> result like<br> this... All Hbonds with Glycine - 1872, All<br> Collisions 704.<br>
Does anyone know how is it possible?<br> I don't know how any of your numbers are possible<br> (1872 H-bonds<br> forming with a glycine?), or what you are defining<br>
as a collision<br> and how you calculated it. Please provide the<br> exact commands that<br> you're using. If you're equating a contact (e.g.<br> from g_mindist)<br>
with a collision, then realize that the default<br> criteria for a<br> contact are very different than the geometric<br> 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>
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<br><br> My system is made of 10 ligands and one protein. I<br> used command:<br> g_hbond -f md.trr -s md.tpr -n res91.ndx -num<br> 91with10LIGbonds.xvg<br> Where I specified in the index file two groups: 10<br>
ligands and<br> Glycine residue. So I have calculated hbonds (second<br> column) and<br> collisions (third column) and then I made a sum of<br> all frames<br>
during 100 ns simualtion time (one frame every 50 ps)<br> obtaining<br> 1872 hbonds and 703 collisions between Glycine and 10<br> ligands. I<br> did it with every residue to assess binding affinity of<br>
different amino acids.<br> Criteria for collision is distance <3.5 A, and fo<br> hbond distance<br> <3.5 A and angle. So when calcualting hbond and<br> collisions the<br>
number of hbonds has has to be smaller while<br> collision takes<br> into account hbonds as welll. I obtained results like<br> this for<br> all other residues which seems to be correct. Am I<br>
right? <br> No. The second column is not inclusive of the first. It<br> counts the<br> number of atoms that are within hydrogen bonding<br> distance, but do<br> not meet the criteria because of the angle between D-H-A.<br>
<br><br> -Justin<br><br> In this case number of collisions has to include number<br> of hbonds.<br> If collision is counted as a distance <3.5 and hbond<br> distance <3.5<br>
plus angle D-H-A means that collisions covers hbonds...<br> Explain<br> please whether I am wrong.<br><br><br> The second column lists the number of atom pairs that satisfy<br> the distance requirement but do not satisfy the angle<br>
requirement and therefore are not hydrogen bonds. The two<br> columns are mutually exclusive. The sum of these two columns<br> would be the total number of pairs that are within<br> hydrogen-bonding distance, but the first column indicates those<br>
that are actually involved in hydrogen bonds (because of the<br> angle), and the second column indicates those that are not<br> involved in hydrogen bonds.<br><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>
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<div class="h5"><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>
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