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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 0da2ef5..b5ac7cb 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 @@ -5,4 +5,4 @@ </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 termianl to only run the next part if the previous command runs succesfuly 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><div id="disqus_thread"></div><script src="/assets/disqus.js"></script><noscript>Please enable JavaScript to view the comments</noscript></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>
\ No newline at end of file +</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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