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diff --git a/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL/index.html b/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL/index.html index b5ac7cb..1140743 100644 --- a/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL/index.html +++ b/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL/index.html @@ -1,4 +1,4 @@ -<!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 src="https://www.googletagmanager.com/gtag/js?id=UA-108635191-1v"></script><script>window.dataLayer = window.dataLayer || [];function gtag(){dataLayer.push(arguments);}gtag('js', new Date());gtag('config', 'UA-108635191-1');</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></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 June 2, 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 +<!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>var _paq=window._paq=window._paq||[];_paq.push(["trackPageView"]),_paq.push(["enableLinkTracking"]),function(){_paq.push(["setTrackerUrl","https://navanchauhan.matomo.cloud/matomo.php"]),_paq.push(["setSiteId","1"]);var a=document,t=a.createElement("script"),e=a.getElementsByTagName("script")[0];t.type="text/javascript",t.async=!0,t.src="//cdn.matomo.cloud/navanchauhan.matomo.cloud/matomo.js",e.parentNode.insertBefore(t,e)}();</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></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 June 2, 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> |