http://wiki.docking.org/index.php?action=history&feed=atom&title=Multimol2db2.py 2026-05-25T13:04:48Z Revision history for this page on the wiki MediaWiki 1.39.1 http://wiki.docking.org/index.php?title=Multimol2db2.py&diff=6172&oldid=prev 2014-02-15T18:00:35Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 18:00, 15 February 2014</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l30">Line 30:</td> <td colspan="2" class="diff-lineno">Line 30:</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;"><br/></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;"><br/></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>[[User:Rgc]]</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>[[User:Rgc]]</div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></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><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></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><ins style="font-weight: bold; text-decoration: none;">[[Category:Software]]</ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></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><ins style="font-weight: bold; text-decoration: none;">[[Category:Databases]]</ins></div></td></tr> <!-- diff cache key wikidb:diff::1.12:old-5711:rev-6172 --> </table>

Frodo http://wiki.docking.org/index.php?title=Multimol2db2.py&diff=5711&oldid=prev 2014-02-07T21:14:06Z

<p>Created page with &quot;&#039;&#039;&#039;multimol2db2.py&#039;&#039;&#039; This script is a utility program that takes as input a .mol2 file that has been protonated and all conformations have been generated with OMEGA (or alte...&quot;</p> <p><b>New page</b></p><div>&#039;&#039;&#039;multimol2db2.py&#039;&#039;&#039;<br /> <br /> This script is a utility program that takes as input a .mol2 file that has been protonated and all conformations have been generated with OMEGA (or alternatively, a mol2 file from some other source) and runs AMSOL &amp; mol2db2 on it to make .db2 files for docking.<br /> <br /> multimol2db2.py input.mol2<br /> <br /> It is very important that the beginning of your .mol2 file contains this kind of header:<br /> <br /> @&lt;TRIPOS&gt;MOLECULE<br /> TEMP12345678<br /> 70 72 0 0 0<br /> SMALL<br /> NO_CHARGES<br /> <br /> @&lt;TRIPOS&gt;ATOM<br /> 1 C1 5.1180 4.5740 2.9690 C.3 1 UNK1 0.0182<br /> 2 N1 4.4470 5.0610 4.2130 N.4 1 UNK1 -0.5553<br /> <br /> Otherwise AMSOL and the associated scripts that run it will crash. The most important part is the second line that needs to be in the form XXXX00000000<br /> <br /> Other tips:<br /> <br /> 1. Don&#039;t have any extra lines except the MOLECULE, ATOM and BOND records<br /> <br /> 2. The last 3 columns of the atom record are important (the 1 UNK1 0.0182), some .mol2 files don&#039;t have them so just add dummy (1 UNK1 0.0000) to yours.<br /> <br /> The file is in your dockenv/src/mol2db2/ or $DOCK_BASE/src/mol2db2<br /> <br /> A version is also kept is ~/Source/rgc_src/multimol2db2.py<br /> <br /> [[User:Rgc]]</div>

Rgc