http://wiki.docking.org/api.php?action=feedcontributions&feedformat=atom&user=DahliaDISI - User contributions [en]2026-05-24T10:58:43ZUser contributionsMediaWiki 1.39.1http://wiki.docking.org/index.php?title=Multimol2db.py&diff=5342Multimol2db.py2013-01-21T18:46:35Z<p>Dahlia: </p>
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<div>'''multimol2db.py'''<br />
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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 & mol2db on it to make .db files for docking.<br />
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multimol2db.py input.mol2<br />
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It is very important that the beginning of your .mol2 file contains this kind of header:<br />
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@<TRIPOS>MOLECULE<br />
TEMP12345678<br />
70 72 0 0 0<br />
SMALL<br />
NO_CHARGES<br />
<br />
@<TRIPOS>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 />
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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 />
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Other tips:<br />
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1. Don't have any extra lines except the MOLECULE, ATOM and BOND records<br />
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2. The last 3 columns of the atom record are important (the 1 UNK1 0.0182), some .mol2 files don't have them so just add dummy (1 UNK1 0.0000) to yours.<br />
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The file is in your dockenv/scripts or $DOCK_BASE/scripts/<br />
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A version is also kept is ~/Source/bks_src/multimol2db.py<br />
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[[User:Rgc]]<br />
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Crucial tip:<br />
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You have to add the correct header to the db.db.gz file:<br />
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DOCK 5.2 ligand_atoms<br />
positive (1)<br />
negative (2)<br />
acceptor (3)<br />
donor (4)<br />
ester_o (5)<br />
amide_o (6)<br />
neutral (7)<br />
<br />
[[User:drw]]</div>Dahlia