https://wiki.csi.cuny.edu/cunyhpc/index.php?action=history&feed=atom&title=Applications_Environment%2Fautodock 2026-05-24T17:36:51Z Revision history for this page on the wiki MediaWiki 1.38.4 https://wiki.csi.cuny.edu/cunyhpc/index.php?title=Applications_Environment/autodock&diff=42&oldid=prev 2022-10-17T17:24:27Z

<p>Created page with &quot;&lt;h1&gt;&lt;b&gt;AUTODOCK&lt;/b&gt;&lt;/h1&gt; &lt;br&gt; __TOC__ &lt;br&gt; &lt;font color=red&gt;&lt;b&gt;Description:&lt;/b&gt;&lt;/font color&gt; &lt;b&gt;&lt;i&gt;AutoDock&lt;/i&gt;&lt;/b&gt; is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. &lt;font color=red&gt;&lt;b&gt;Additional Notes:&lt;/b&gt;&lt;/font color&gt; Current distributions of &lt;b&gt;&lt;i&gt;AutoDock&lt;/i&gt;&lt;/b&gt; consist of two generations of software: &lt;b&gt;&lt;i&gt;AutoDock 4&lt;/i&gt;&lt;/b&gt; and &lt;b&gt;&lt;i&gt;AutoDock Vina...&quot;</p> <p><b>New page</b></p><div>&lt;h1&gt;&lt;b&gt;AUTODOCK&lt;/b&gt;&lt;/h1&gt;<br /> &lt;br&gt;<br /> __TOC__<br /> &lt;br&gt;<br /> &lt;font color=red&gt;&lt;b&gt;Description:&lt;/b&gt;&lt;/font color&gt; &lt;b&gt;&lt;i&gt;AutoDock&lt;/i&gt;&lt;/b&gt; is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. <br /> <br /> &lt;font color=red&gt;&lt;b&gt;Additional Notes:&lt;/b&gt;&lt;/font color&gt; Current distributions of &lt;b&gt;&lt;i&gt;AutoDock&lt;/i&gt;&lt;/b&gt; consist of two generations of software: &lt;b&gt;&lt;i&gt;AutoDock 4&lt;/i&gt;&lt;/b&gt; and &lt;b&gt;&lt;i&gt;AutoDock Vina&lt;/i&gt;&lt;/b&gt;. The latter is a new generation of docking software from the Molecular Graphics Lab. It achieves significant improvements in the average accuracy of the binding mode predictions, while also being up to two orders of magnitude faster than &lt;b&gt;&lt;i&gt;AutoDock 4.1&lt;/i&gt;&lt;/b&gt;.<br /> <br /> Because the scoring functions used by &lt;b&gt;&lt;i&gt;AutoDock 4&lt;/i&gt;&lt;/b&gt; and &lt;b&gt;&lt;i&gt;AutoDock Vina&lt;/i&gt;&lt;/b&gt; are different and inexact, on any given problem, either program may provide a better result. <br /> <br /> Please note that preparing the input files for &lt;b&gt;&lt;i&gt;AutoDock 4&lt;/i&gt;&lt;/b&gt; require use of &lt;b&gt;&lt;i&gt;Autodock&lt;/i&gt;&lt;/b&gt; tool set. The use of the later is not described in this document. <br /> <br /> &lt;font color=red&gt;&lt;b&gt;Availability:&lt;/b&gt;&lt;/font color&gt; PENZIAS and ANDY<br /> <br /> &lt;font color=red&gt;&lt;b&gt;Module file:&lt;/b&gt;&lt;/font color&gt; autodock<br /> <br /> &lt;font color=red&gt;&lt;b&gt;Limitations:&lt;/b&gt;&lt;/font color&gt; &lt;b&gt;&lt;i&gt;AutoDock&lt;/i&gt;&lt;/b&gt; is distributed freely under the GNU GPL for all to use. AutoDock Vina is available under the Apache license, allowing commercial and non-commercial use and redistribution.<br /> <br /> &lt;font color=red&gt;&lt;b&gt;Citation:&lt;/b&gt;&lt;/font color&gt; Include in published paper the following citation regarding use of:<br /> ::&lt;br&gt;&lt;b&gt;&lt;i&gt; AutoDock&lt;/i&gt;&lt;/b&gt;: Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S. and Olson, A. J. (2009) &lt;br&gt;<br /> ::&lt;b&gt;&lt;i&gt;Autodock4&lt;/i&gt;&lt;/b&gt; and &lt;b&gt;&lt;i&gt;AutoDockTools4&lt;/i&gt;&lt;/b&gt;: automated docking with selective receptor flexiblity. J. Computational Chemistry 2009, 16: 2785-91. &lt;br&gt;<br /> ::Morris, G. M., Goodsell, D. S., Halliday, R.S., Huey, R., Hart, W. E., Belew, R. K. and Olson, A. J. (1998), Automated Docking Using a Lamarckian Genetic Algorithm and and Empirical Binding Free Energy Function J. Computational Chemistry, 19: 1639-1662. &lt;br&gt;<br /> ::&lt;b&gt;&lt;i&gt;AutoDock Vina:&lt;/i&gt;&lt;/b&gt; O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry 31 (2010) 455-461<br /> <br /> <br /> &lt;font color=red&gt;&lt;b&gt;Documentation:&lt;/b&gt;&lt;/font color&gt;<br /> http://autodock.scripps.edu/faqs-help/manual/autodock-4-2-user-guide&lt;br&gt;<br /> ::http://autodock.scripps.edu/faqs-help/manual/autodock-vina-manual-page/autodock-vina-manual-page &lt;br&gt;<br /> &lt;font color=red&gt;&lt;b&gt;Tutorials:&lt;/b&gt;&lt;/font color&gt; http://autodock.scripps.edu/faqs-help/tutorial<br /> <br /> &lt;font color=red&gt;&lt;b&gt;Related Packages:&lt;/b&gt;&lt;/font color&gt;<br /> ::Pardock<br /> ::ICM<br /> ::SwissDock<br /> <br /> &lt;font color=red&gt;&lt;b&gt;Use:&lt;/b&gt;&lt;/font color&gt; Load module file.<br /> &lt;font face=&quot;courier&quot;&gt; <br /> module load autodock <br /> &lt;/font&gt;<br /> <br /> &lt;font color=red&gt;&lt;b&gt;Example:&lt;/b&gt;&lt;/font color&gt;<br /> &lt;b&gt;&lt;i&gt;Autodock&lt;/i&gt;&lt;/b&gt; example requires several files, which are prepared &lt;b&gt;&lt;i&gt;Autodock&lt;/i&gt;&lt;/b&gt; tool set and placed in &lt;font face=&quot;courier&quot;&gt;&lt;b&gt;/share/apps/autodock/default/example/in&lt;/b&gt;&lt;/font&gt; directory. Upon running the example the files from this directory must be copied in a user directory by the command:<br /> <br /> cp /share/apps/autodock/default/example/in/* .<br /> <br /> Below is given an example of job submitting script. Please note that installed version of &lt;b&gt;&lt;i&gt;Autodock&lt;/i&gt;&lt;/b&gt; is a serial program, so the fields &lt;font face=&quot;courier&quot;&gt;&lt;b&gt;&lt;cpus&gt;&lt;/b&gt;&lt;/font&gt; and &lt;font face=&quot;courier&quot;&gt;&lt;b&gt;&lt;chunks&gt;&lt;/b&gt;&lt;/font&gt; must have value of &lt;font face=&quot;courier&quot;&gt;&lt;b&gt;1&lt;/b&gt;&lt;/font&gt;. The file &lt;font face=&quot;courier&quot;&gt;&lt;b&gt;aq.dpf&lt;/b&gt;&lt;/font&gt; below is called &lt;b&gt;&lt;i&gt;docking parameter file&lt;/i&gt;&lt;/b&gt; and is generated by &lt;b&gt;&lt;i&gt;themkgpf3&lt;/i&gt;&lt;/b&gt; and &lt;b&gt;&lt;i&gt;mkdpf3&lt;/i&gt;&lt;/b&gt; programs, which are part of &lt;b&gt;&lt;i&gt;Autodock&lt;/i&gt;&lt;/b&gt; tool set.<br /> <br /> ==PENZIAS or ANDY==<br /> <br /> #!/bin/bash <br /> #SBATCH -- autodock_test <br /> #SBATCH -- partition production <br /> #SBATCH -- select=&lt;font color=&quot;red&quot;&gt;&lt;chunks&gt;&lt;/font color&gt;<br /> #SBATCH -- tasks=&lt;font color=&quot;red&quot;&gt;&lt;cpus&gt;&lt;/font color&gt; <br /> <br /> # Explicitly change to the working directory <br /> cd $SLURM_SUBMIT_DIR <br /> <br /> # generate atomic maps <br /> <br /> autogrid4 -p aq.gpf -l output_mapGeneration.glg <br /> <br /> # execute autodock <br /> <br /> autodock4 -p aq.dpf -l output_autodock.dlg #------------------------------ echo &quot;*** Job is done! ***&quot;</div>

James