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<!DOCTYPE html><html lang="en"><head><meta charset="UTF-8"/><meta name="og:site_name" content="Navan Chauhan"/><link rel="canonical" href="https://navanchauhan.github.io/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL"/><meta name="twitter:url" content="https://navanchauhan.github.io/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL"/><meta name="og:url" content="https://navanchauhan.github.io/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL"/><title>Workflow for Lightning Fast Molecular Docking Part One | Navan Chauhan</title><meta name="twitter:title" content="Workflow for Lightning Fast Molecular Docking Part One | Navan Chauhan"/><meta name="og:title" content="Workflow for Lightning Fast Molecular Docking Part One | Navan Chauhan"/><meta name="description" content="This is my workflow for lightning fast molecular docking."/><meta name="twitter:description" content="This is my workflow for lightning fast molecular docking."/><meta name="og:description" content="This is my workflow for lightning fast molecular docking."/><meta name="twitter:card" content="summary"/><link rel="stylesheet" href="/styles.css" type="text/css"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><link rel="shortcut icon" href="/images/favicon.png" type="image/png"/><link rel="alternate" href="/feed.rss" type="application/rss+xml" title="Subscribe to Navan Chauhan"/><meta name="twitter:image" content="https://navanchauhan.github.io/images/logo.png"/><meta name="og:image" content="https://navanchauhan.github.io/images/logo.png"/></head><head><script async src="//gc.zgo.at/count.js" data-goatcounter="https://navanchauhan.goatcounter.com/count"></script></head><body class="item-page"><header><div class="wrapper"><a class="site-name" href="/">Navan Chauhan</a><nav><ul><li><a href="/about">About Me</a></li><li><a class="selected" href="/posts">Posts</a></li><li><a href="/publications">Publications</a></li><li><a href="/assets/résumé.pdf">Résumé</a></li><li><a href="https://navanchauhan.github.io/repo">Repo</a></li><li><a href="/feed.rss">RSS Feed</a></li></ul></nav></div></header><div class="wrapper"><article><div class="content"><span class="reading-time">2 minute read</span><span class="reading-time">Created on June 1, 2020</span><span class="reading-time">Last modified on September 15, 2020</span><h1>Workflow for Lightning Fast Molecular Docking Part One</h1><h2>My Setup</h2><ul><li>macOS Catalina ( RIP 32bit app)</li><li>PyMOL</li><li>AutoDock Vina</li><li>Open Babel</li></ul><h2>One Command Docking</h2><pre><code><div class="highlight"><span></span>obabel -:<span class="s2">"</span><span class="k">$(</span>pbpaste<span class="k">)</span><span class="s2">"</span> --gen3d -opdbqt -Otest.pdbqt <span class="o">&&</span> vina --receptor lu.pdbqt --center_x -9.7 --center_y <span class="m">11</span>.4 --center_z <span class="m">68</span>.9 --size_x <span class="m">19</span>.3 --size_y <span class="m">29</span>.9 --size_z <span class="m">21</span>.3 --ligand test.pdbqt
</div></code></pre><p>To run this command you simple copy the SMILES structure of the ligand you want an it automatically takes it from your clipboard, generates the 3D structure in the AutoDock PDBQT format using Open Babel and then docks it with your receptor using AutoDock Vina, all with just one command.</p><p>Let me break down the commands</p><pre><code><div class="highlight"><span></span>obabel -:<span class="s2">"</span><span class="k">$(</span>pbpaste<span class="k">)</span><span class="s2">"</span> --gen3d -opdbqt -Otest.pdbqt
</div></code></pre><p><code>pbpaste</code> and <code>pbcopy</code> are macOS commands for pasting and copying from and to the clipboard. Linux users may install the <code>xclip</code> and <code>xsel</code> packages from their respective package managers and then insert these aliases into their bash_profile, zshrc e.t.c</p><pre><code><div class="highlight"><span></span><span class="nb">alias</span> <span class="nv">pbcopy</span><span class="o">=</span><span class="s1">'xclip -selection clipboard'</span>
<span class="nb">alias</span> <span class="nv">pbpaste</span><span class="o">=</span><span class="s1">'xclip -selection clipboard -o'</span>
</div></code></pre><pre><code><div class="highlight"><span></span><span class="k">$(</span>pbpaste<span class="k">)</span>
</div></code></pre><p>This is used in bash to evaluate the results of a command. In this scenario we are using it to get the contents of the clipboard.</p><p>The rest of the command is a normal Open Babel command to generate a 3D structure in PDBQT format and then save it as <code>test.pdbqt</code></p><pre><code><div class="highlight"><span></span><span class="o">&&</span>
</div></code></pre><p>This tells the terminal to only run the next part if the previous command runs successfully without any errors.</p><pre><code><div class="highlight"><span></span>vina --receptor lu.pdbqt --center_x -9.7 --center_y <span class="m">11</span>.4 --center_z <span class="m">68</span>.9 --size_x <span class="m">19</span>.3 --size_y <span class="m">29</span>.9 --size_z <span class="m">21</span>.3 --ligand test.pdbqt
</div></code></pre><p>This is just the docking command for AutoDock Vina. In the next part I will tell how to use PyMOL and a plugin to directly generate the coordinates in Vina format <code> --center_x -9.7 --center_y 11.4 --center_z 68.9 --size_x 19.3 --size_y 29.9 --size_z 21.3</code> without needing to type them manually.</p></div><span>Tagged with: </span><ul class="tag-list"><li><a href="/tags/codesnippet">Code-Snippet</a></li><li><a href="/tags/moleculardocking">Molecular-Docking</a></li><li><a href="/tags/cheminformatics">Cheminformatics</a></li><li><a href="/tags/openbabel">Open-Babel</a></li><li><a href="/tags/autodock-vina">AutoDock Vina</a></li></ul></article></div><footer><p>Made with ❤️ using <a href="https://github.com/johnsundell/publish">Publish</a></p><p><a href="/feed.rss">RSS feed</a></p></footer></body></html>
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