diff options
Diffstat (limited to 'docs/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html')
| -rw-r--r-- | docs/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html | 75 |
1 files changed, 54 insertions, 21 deletions
diff --git a/docs/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html b/docs/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html index 4d6e540..32abeda 100644 --- a/docs/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html +++ b/docs/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html @@ -2,14 +2,27 @@ <html lang="en"> <head> - <link rel="stylesheet" href="https://unpkg.com/latex.css/style.min.css" /> + <meta http-equiv="X-UA-Compatible" content="IE=edge"> + <meta http-equiv="content-type" content="text/html; charset=utf-8"> + <meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1"> + <meta name="theme-color" content="#6a9fb5"> + + <title>Workflow for Lightning Fast Molecular Docking Part One</title> + + <!-- + <link rel="stylesheet" href="https://unpkg.com/latex.css/style.min.css" /> + --> + + <link rel="stylesheet" href="/assets/c-hyde.css" /> + + <link rel="stylesheet" href="http://fonts.googleapis.com/css?family=PT+Sans:400,400italic,700|Abril+Fatface"> + <link rel="stylesheet" href="/assets/main.css" /> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> - <title>Workflow for Lightning Fast Molecular Docking Part One</title> <meta name="og:site_name" content="Navan Chauhan" /> <link rel="canonical" href="https://web.navan.dev/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html" /> - <meta name="twitter:url" content="https://web.navan.dev/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html /> + <meta name="twitter:url" content="https://web.navan.dev/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html" /> <meta name="og:url" content="https://web.navan.dev/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html" /> <meta name="twitter:title" content="Workflow for Lightning Fast Molecular Docking Part One" /> <meta name="og:title" content="Workflow for Lightning Fast Molecular Docking Part One" /> @@ -26,26 +39,45 @@ <script data-goatcounter="https://navanchauhan.goatcounter.com/count" async src="//gc.zgo.at/count.js"></script> <script defer data-domain="web.navan.dev" src="https://plausible.io/js/plausible.js"></script> - <link rel="manifest" href="manifest.json" /> + <link rel="manifest" href="/manifest.json" /> </head> -<body> - <center><nav style="display: block;"> -| -<a href="/">home</a> | -<a href="/about/">about/links</a> | -<a href="/posts/">posts</a> | -<!--<a href="/publications/">publications</a> |--> -<!--<a href="/repo/">iOS repo</a> |--> -<a href="/feed.rss">RSS Feed</a> | -</nav> -</center> +<body class="theme-base-0d"> + <div class="sidebar"> + <div class="container sidebar-sticky"> + <div class="sidebar-about"> + <h1><a href="/">Navan</a></h1> + <p class="lead" id="random-lead">Alea iacta est.</p> + </div> + + <ul class="sidebar-nav"> + <li><a class="sidebar-nav-item" href="/about/">about/links</a></li> + <li><a class="sidebar-nav-item" href="/posts/">posts</a></li> + <li><a class="sidebar-nav-item" href="/3D-Designs/">3D designs</a></li> + <li><a class="sidebar-nav-item" href="/feed.rss">RSS Feed</a></li> + <li><a class="sidebar-nav-item" href="/colophon/">colophon</a></li> + </ul> + <div class="copyright"><p>© 2019-2024. Navan Chauhan <br> <a href="/feed.rss">RSS</a></p></div> + </div> +</div> + +<script> +let phrases = [ + "Something Funny", "Veni, vidi, vici", "Alea iacta est", "In vino veritas", "Acta, non verba", "Castigat ridendo mores", + "Cui bono?", "Memento vivere", "अहम् ब्रह्मास्मि", "अनुगच्छतु प्रवाहं", "चरन्मार्गान्विजानाति", "coq de cheval", "我愛啤酒" + ]; + +let new_phrase = phrases[Math.floor(Math.random()*phrases.length)]; + +let lead = document.getElementById("random-lead"); +lead.innerText = new_phrase; +</script> + <div class="content container"> -<main> - - <h1>Workflow for Lightning Fast Molecular Docking Part One</h1> + <div class="post"> + <h1 id="workflow-for-lightning-fast-molecular-docking-part-one">Workflow for Lightning Fast Molecular Docking Part One</h1> -<h2>My Setup</h2> +<h2 id="my-setup">My Setup</h2> <ul> <li>macOS Catalina ( RIP 32bit app)</li> @@ -54,7 +86,7 @@ <li>Open Babel</li> </ul> -<h2>One Command Docking</h2> +<h2 id="one-command-docking">One Command Docking</h2> <pre><code>obabel -:"$(pbpaste)" --gen3d -opdbqt -Otest.pdbqt && vina --receptor lu.pdbqt --center_x -9.7 --center_y 11.4 --center_z 68.9 --size_x 19.3 --size_y 29.9 --size_z 21.3 --ligand test.pdbqt </code></pre> @@ -89,14 +121,15 @@ alias pbpaste='xclip -selection clipboard -o' <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> <blockquote>If you have scrolled this far, consider subscribing to my mailing list <a href="https://listmonk.navan.dev/subscription/form">here.</a> You can subscribe to either a specific type of post you are interested in, or subscribe to everything with the "Everything" list.</blockquote> <script data-isso="https://comments.navan.dev/" src="https://comments.navan.dev/js/embed.min.js"></script> <section id="isso-thread"> <noscript>Javascript needs to be activated to view comments.</noscript> </section> -</main> + </div> <script src="assets/manup.min.js"></script> <script src="/pwabuilder-sw-register.js"></script> </body> |