BKS lab Structure preparation - Revision history

TBalius: /* Preparing cofactors or nonstandard residue for receptor */

2014-03-14T12:42:18Z

Preparing cofactors or nonstandard residue for receptor

← Older revision		Revision as of 12:42, 14 March 2014
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	file2file.py LZ6.pdb LZ6.mol2		file2file.py LZ6.pdb LZ6.mol2

	~~the~~ script file2file.py is an addon to convert.py (which is supplied by open eye) that is:		The script file2file.py is an addon to convert.py (which is supplied by open eye) that is:
	(A) more stringent on keeping original atom names, and		(A) more stringent on keeping original atom names, and
	(B) the only script able to convert to and from test.eel1 format.		(B) the only script able to convert to and from test.eel1 format.

2014-03-14T12:41:46Z

← Older revision		Revision as of 12:41, 14 March 2014
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	charge_cofactor.csh LZ6.mol2 LZ6 hydrogens		charge_cofactor.csh LZ6.mol2 LZ6 hydrogens

	by adding the word "hydrogens" the end of the command the hydrogens will also be included ~~in the~~		by adding the word "hydrogens" the end of the command the hydrogens will also be included.

	~~the~~ output of this command is LZ6.prot.table		The output of this command is LZ6.prot.table

	which you should add the the prot.table in grids and then run:		which you should add the the prot.table in grids and then run:

2014-03-11T00:06:00Z

← Older revision		Revision as of 00:06, 11 March 2014
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	[[Category:Tutorials]]		[[Category:Tutorials]]
	[[Category:~~Docking~~]]		[[Category:DOCK]]
	[[Category:~~Incomplete]]~~		[[Category:Obsolete]]
	~~[[Category:Suspected obsolete~~]]

2014-02-14T02:54:06Z

← Older revision		Revision as of 02:54, 14 February 2014
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	== perparing ligands for docking ==		== perparing ligands for docking ==



			[[Category:Tutorials]]
			[[Category:Docking]]
			[[Category:Incomplete]]
			[[Category:Suspected obsolete]]

2013-01-23T22:34:31Z

← Older revision		Revision as of 22:34, 23 January 2013
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	The co-factor needs to be in the rec.pdb and rec.crg. The cofactor should be included as part of the receptors and needs parameters so that Electrostatic, Solvation, VDW grids can be calculated. To calculate the VDW types and charges call the following scripts:		The co-factor needs to be in the rec.pdb and rec.crg. The cofactor should be included as part of the receptors and needs parameters so that Electrostatic, Solvation, VDW grids can be calculated. To calculate the VDW types and charges call the following scripts:

	The script "charge_cofactor.csh" that takes as input a mol2 file with very strict mol2 naming		The script "charge_cofactor.csh" that takes as input a mol2 file with very strict mol2 naming.

	You will need to have Ligand pdb file ( LZ6.pdb ). This file should have hydrogen.		You will need to have Ligand pdb file ( LZ6.pdb ). This file should have hydrogen.

2013-01-23T22:34:13Z

← Older revision		Revision as of 22:34, 23 January 2013
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	Adding a cofactor to DOCK		Adding a cofactor to DOCK

	~~first you need the~~ co-factor to be in the rec.pdb ~~(Actually the~~ rec.crg) so that ~~solvation could~~ be calculated ~~on it~~. To ~~take care of~~ VDW ~~typing~~ and charges ~~there's a~~ scripts ~~called~~:		The co-factor needs to be in the rec.pdb and rec.crg. The cofactor should be included as part of the receptors and needs parameters so that Electrostatic, Solvation, VDW grids can be calculated. To calculate the VDW types and charges call the following scripts:

	~~$mud/~~charge_cofactor.csh that takes as input a mol2 file with very strict mol2 naming		The script "charge_cofactor.csh" that takes as input a mol2 file with very strict mol2 naming

	You will need to have Ligand pdb file ( LZ6.pdb )		You will need to have Ligand pdb file ( LZ6.pdb ). This file should have hydrogen.

	isssue the following command:		isssue the following command:

2013-01-22T19:24:21Z

Preparing cofactors or nonstandard residue for receptor

← Older revision		Revision as of 19:24, 22 January 2013
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	modify the prot.table and create amb and now you can also add the coordinates directly to rec.crg - do this and re-make.		modify the prot.table and create amb and now you can also add the coordinates directly to rec.crg - do this and re-make.

			If you have confidence in your preparation then you can add the prot.table to the library:

	~~If you have confidence in your preporation then you can add the prot.table to the libary:~~		code/dockenv/trunk/scripts/grids/

	~~code/dockenv/trunk/scripts/grids/~~		This will allow others to uses this preparation with the automated scripts.

	This will allow others to uses this ~~preperation~~ with the automated scripts.

	== perparing ligands for docking ==		== perparing ligands for docking ==

2013-01-22T19:21:38Z

← Older revision		Revision as of 19:21, 22 January 2013
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	modify the prot.table and create amb and now you can also add the coordinates directly to rec.crg - do this and re-make.		modify the prot.table and create amb and now you can also add the coordinates directly to rec.crg - do this and re-make.


			If you have confidence in your preporation then you can add the prot.table to the libary:

			code/dockenv/trunk/scripts/grids/

			This will allow others to uses this preperation with the automated scripts.

	== perparing ligands for docking ==		== perparing ligands for docking ==

2013-01-02T23:13:13Z

Preparing cofactors or nonstandard residue for receptor

← Older revision		Revision as of 23:13, 2 January 2013
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	$mud/charge_cofactor.csh LZ6.mol2 LZ6		$mud/charge_cofactor.csh LZ6.mol2 LZ6

	charge_cofactor.csh ~~input~~.mol2 ~~RES~~ hydrogens		charge_cofactor.csh LZ6.mol2 LZ6 hydrogens

	by adding the word "hydrogens" the end of the command the hydrogens will also be included in the		by adding the word "hydrogens" the end of the command the hydrogens will also be included in the
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	Then:		Then:

	first run make ~~w/o~~ the co-factor, you can kill it when it starts solvation calculations		first run make with out the co-factor, you can kill it when it starts solvation calculations

	modify the prot.table and create amb and now you can also add the coordinates directly to rec.crg - do this and re-make.		modify the prot.table and create amb and now you can also add the coordinates directly to rec.crg - do this and re-make.

	== perparing ligands for docking ==		== perparing ligands for docking ==

2013-01-02T23:11:54Z

Preparing cofactors or nonstandard residue for receptor

← Older revision		Revision as of 23:11, 2 January 2013
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	file2file.py LZ6.pdb LZ6.mol2		file2file.py LZ6.pdb LZ6.mol2

	(file2file is an addon to convert.py (which is supplied by open eye) that is: (A) more stringent on keeping original atom names, and (B) the only script able to convert to and from test.eel1 format.		the script file2file.py is an addon to convert.py (which is supplied by open eye) that is:
			(A) more stringent on keeping original atom names, and
			(B) the only script able to convert to and from test.eel1 format.

	If you want to score a native ligand you should first convert it to test.eel1 using file2file.py and than you can use doscoreopt.sh on it.		If you want to score a native ligand you should first convert it to test.eel1 using file2file.py and than you can use doscoreopt.sh on it.