Multimol2db.py - Revision history

Frodo at 01:03, 11 March 2014

2014-03-11T01:03:50Z

← Older revision		Revision as of 01:03, 11 March 2014
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	neutral (7)		neutral (7)

	~~[[User:drw]]~~
	[[Category:Docking]]		[[Category:Docking]]
	[[Category:~~Database preparation~~]]		[[Category:Software]]

2014-02-14T03:50:01Z

← Older revision		Revision as of 03:50, 14 February 2014
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	[[User:drw]]		[[User:drw]]
			[[Category:Docking]]
			[[Category:Database preparation]]

2013-01-21T18:46:35Z

← Older revision		Revision as of 18:46, 21 January 2013
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	[[User:Rgc]]		[[User:Rgc]]

			Crucial tip:

			You have to add the correct header to the db.db.gz file:

			DOCK 5.2 ligand_atoms
			positive (1)
			negative (2)
			acceptor (3)
			donor (4)
			ester_o (5)
			amide_o (6)
			neutral (7)

			[[User:drw]]

2012-10-08T20:29:23Z

5 revisions

← Older revision

Revision as of 20:29, 8 October 2012

2012-02-08T01:00:23Z

added some tips to get this to work from Nir

← Older revision		Revision as of 01:00, 8 February 2012
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	SMALL		SMALL
	NO_CHARGES		NO_CHARGES

	@<TRIPOS>ATOM		@<TRIPOS>ATOM
			1 C1 5.1180 4.5740 2.9690 C.3 1 UNK1 0.0182
			2 N1 4.4470 5.0610 4.2130 N.4 1 UNK1 -0.5553

	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		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

			Other tips:

			1. Don't have any extra lines except the MOLECULE, ATOM and BOND records

			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.

	The file is in your dockenv/scripts or $DOCK_BASE/scripts/		The file is in your dockenv/scripts or $DOCK_BASE/scripts/

2012-02-06T18:51:22Z

explaining how henry broke everything

← Older revision		Revision as of 18:51, 6 February 2012
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	It is very important that the beginning of your .mol2 file contains this kind of header:		It is very important that the beginning of your .mol2 file contains this kind of header:

			@<TRIPOS>MOLECULE
			TEMP12345678
			70 72 0 0 0
			SMALL
			NO_CHARGES

			@<TRIPOS>ATOM

			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

	The file is in your dockenv/scripts or $DOCK_BASE/scripts/		The file is in your dockenv/scripts or $DOCK_BASE/scripts/

2012-02-06T18:50:07Z

← Older revision		Revision as of 18:50, 6 February 2012
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	multimol2db.py input.mol2		multimol2db.py input.mol2

			It is very important that the beginning of your .mol2 file contains this kind of header:



	The file is in your dockenv/scripts or $DOCK_BASE/scripts/		The file is in your dockenv/scripts or $DOCK_BASE/scripts/

2012-02-03T22:27:58Z

← Older revision		Revision as of 22:27, 3 February 2012
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	'''multimol2db.py'''		'''multimol2db.py'''

	This script runs		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.

			multimol2db.py input.mol2

			The file is in your dockenv/scripts or $DOCK_BASE/scripts/

			A version is also kept is ~/Source/bks_src/multimol2db.py

			[[User:Rgc]]

2012-02-03T22:26:39Z

New page

'''multimol2db.py'''

This script runs