http://wiki.docking.org/index.php?title=Running_DOCK&feed=atom&action=historyRunning DOCK - Revision history2024-03-28T08:32:25ZRevision history for this page on the wikiMediaWiki 1.39.1http://wiki.docking.org/index.php?title=Running_DOCK&diff=4284&oldid=prevTherese: 7 revisions2012-10-08T20:32:23Z<p>7 revisions</p>
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</td></tr></table>Theresehttp://wiki.docking.org/index.php?title=Running_DOCK&diff=4283&oldid=prevMysinger: /* Running DOCK */2011-09-20T23:58:46Z<p><span dir="auto"><span class="autocomment">Running DOCK</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*modify <tt>INDOCK</tt> <del style="font-weight: bold; text-decoration: none;"> </del>and set up the desired directory structure &ndash; either manually or by running '<tt>md4db.csh bysubset N<sub>1</sub> N<sub>2</sub> Type</tt>', where <tt>N<sub>1</sub></tt> is the identifier of the library (1: lead-like; 2: fragment-like), <tt>N<sub>2</sub></tt> is the number of chunks (i.e., jobs you can run in parallel), and <tt>Type</tt> is the category of library (i.e., bysubset, byvendor, etc).</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>*modify <tt><ins style="font-weight: bold; text-decoration: none;">$mud/</ins>INDOCK</tt> and set up the desired directory structure &ndash; either manually or by running '<tt>md4db.csh bysubset N<sub>1</sub> N<sub>2</sub> Type</tt>', where <tt>N<sub>1</sub></tt> is the identifier of the library (1: lead-like; 2: fragment-like), <tt>N<sub>2</sub></tt> is the number of chunks (i.e., jobs you can run in parallel), and <tt>Type</tt> is the category of library (i.e., bysubset, byvendor, etc).</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* if it hasn't been generated by a script, create the file <tt>dirlist</tt>, which conatins the list of the directories (i.e., chunks of the database) that you want to dock.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* if it hasn't been generated by a script, create the file <tt>dirlist</tt>, which conatins the list of the directories (i.e., chunks of the database) that you want to dock.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*if you plan to use any of John's scripts in the downstream processing, leave the output file prefixes at <tt>test.</tt>. </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*if you plan to use any of John's scripts in the downstream processing, leave the output file prefixes at <tt>test.</tt>. </div></td></tr>
</table>Mysingerhttp://wiki.docking.org/index.php?title=Running_DOCK&diff=4282&oldid=prevMysinger: /* Running DOCK */2009-12-05T02:56:41Z<p><span dir="auto"><span class="autocomment">Running DOCK</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 02:56, 5 December 2009</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*modify <tt>INDOCK</tt> and set up the desired directory structure &ndash; either manually or by running <tt>md4db.csh bysubset N<sub>1</sub> N<sub>2</sub> Type</tt>, where <tt>N<sub>1</sub></tt> is the identifier of the library (1: lead-like; 2: fragment-like), <tt>N<sub>2</sub></tt> is the number of chunks (i.e., jobs you can run in parallel), and <tt>Type</tt> is the category of library (i.e., bysubset, byvendor, etc).</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>*modify <tt>INDOCK</tt> and set up the desired directory structure &ndash; either manually or by running <ins style="font-weight: bold; text-decoration: none;">'</ins><tt>md4db.csh bysubset N<sub>1</sub> N<sub>2</sub> Type</tt><ins style="font-weight: bold; text-decoration: none;">'</ins>, where <tt>N<sub>1</sub></tt> is the identifier of the library (1: lead-like; 2: fragment-like), <tt>N<sub>2</sub></tt> is the number of chunks (i.e., jobs you can run in parallel), and <tt>Type</tt> is the category of library (i.e., bysubset, byvendor, etc).</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* if it hasn't been generated by a script, create the file <tt>dirlist</tt>, which conatins the list of the directories (i.e., chunks of the database) that you want to dock.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* if it hasn't been generated by a script, create the file <tt>dirlist</tt>, which conatins the list of the directories (i.e., chunks of the database) that you want to dock.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*if you plan to use any of John's scripts in the downstream processing, leave the output file prefixes at <tt>test.</tt>. </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*if you plan to use any of John's scripts in the downstream processing, leave the output file prefixes at <tt>test.</tt>. </div></td></tr>
</table>Mysingerhttp://wiki.docking.org/index.php?title=Running_DOCK&diff=4281&oldid=prevMysinger: /* Running DOCK */2009-12-05T02:56:27Z<p><span dir="auto"><span class="autocomment">Running DOCK</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*modify <tt>INDOCK</tt> and set up the desired directory structure &ndash; either manually or by running <tt><del style="font-weight: bold; text-decoration: none;">mksdir3</del>.csh N<sub>1</sub> N<sub>2</sub> Type</tt>, where <tt>N<sub>1</sub></tt> is the identifier of the library (1: lead-like; 2: fragment-like), <tt>N<sub>2</sub></tt> is the number of chunks (i.e., jobs you can run in parallel), and <tt>Type</tt> is the category of library (i.e., bysubset, byvendor, etc).</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>*modify <tt>INDOCK</tt> and set up the desired directory structure &ndash; either manually or by running <tt><ins style="font-weight: bold; text-decoration: none;">md4db</ins>.csh <ins style="font-weight: bold; text-decoration: none;">bysubset </ins>N<sub>1</sub> N<sub>2</sub> Type</tt>, where <tt>N<sub>1</sub></tt> is the identifier of the library (1: lead-like; 2: fragment-like), <tt>N<sub>2</sub></tt> is the number of chunks (i.e., jobs you can run in parallel), and <tt>Type</tt> is the category of library (i.e., bysubset, byvendor, etc).</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* if it hasn't been generated by a script, create the file <tt>dirlist</tt>, which conatins the list of the directories (i.e., chunks of the database) that you want to dock.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* if it hasn't been generated by a script, create the file <tt>dirlist</tt>, which conatins the list of the directories (i.e., chunks of the database) that you want to dock.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*if you plan to use any of John's scripts in the downstream processing, leave the output file prefixes at <tt>test.</tt>. </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*if you plan to use any of John's scripts in the downstream processing, leave the output file prefixes at <tt>test.</tt>. </div></td></tr>
</table>Mysingerhttp://wiki.docking.org/index.php?title=Running_DOCK&diff=4280&oldid=prevMysinger at 02:55, 5 December 20092009-12-05T02:55:58Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 02:55, 5 December 2009</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*take care that the paths to the <tt>.db.gz</tt> files in <tt>split_database_index</tt> do not get too long. If they do, go via links. </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*take care that the paths to the <tt>.db.gz</tt> files in <tt>split_database_index</tt> do not get too long. If they do, go via links. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*submit the calculations to the cluster with <tt>$mud/submit.csh</tt> from the directory in which your data (most importantly, <tt>dirlist</tt>) resides. See [[MUD - Michael's Utilities for Docking]] for setting the $mud variable.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*submit the calculations to the cluster with <tt>$mud/submit.csh</tt> from the directory in which your data (most importantly, <tt>dirlist</tt>) resides. See [[MUD - Michael's Utilities for Docking]] for setting the $mud variable.</div></td></tr>
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</table>Mysingerhttp://wiki.docking.org/index.php?title=Running_DOCK&diff=4279&oldid=prevMysinger: /* Running DOCK */2009-12-05T02:28:43Z<p><span dir="auto"><span class="autocomment">Running DOCK</span></span></p>
<p><b>New page</b></p><div>=Running DOCK=<br />
<br />
*modify <tt>INDOCK</tt> and set up the desired directory structure &ndash; either manually or by running <tt>mksdir3.csh N<sub>1</sub> N<sub>2</sub> Type</tt>, where <tt>N<sub>1</sub></tt> is the identifier of the library (1: lead-like; 2: fragment-like), <tt>N<sub>2</sub></tt> is the number of chunks (i.e., jobs you can run in parallel), and <tt>Type</tt> is the category of library (i.e., bysubset, byvendor, etc).<br />
* if it hasn't been generated by a script, create the file <tt>dirlist</tt>, which conatins the list of the directories (i.e., chunks of the database) that you want to dock.<br />
*if you plan to use any of John's scripts in the downstream processing, leave the output file prefixes at <tt>test.</tt>. <br />
*take care that the paths to the <tt>.db.gz</tt> files in <tt>split_database_index</tt> do not get too long. If they do, go via links. <br />
*submit the calculations to the cluster with <tt>$mud/submit.csh</tt> from the directory in which your data (most importantly, <tt>dirlist</tt>) resides. See [[MUD - Michael's Utilities for Docking]] for setting the $mud variable.<br />
[[Category:Manual_DOCK]]</div>Mysinger