INDOCK for DOCK 3.6 - Revision history

Frodo at 18:09, 15 February 2014

2014-02-15T18:09:46Z

2012-10-08T20:27:50Z

11 revisions

← Older revision

Revision as of 20:27, 8 October 2012

2011-12-15T23:13:42Z

← Older revision		Revision as of 23:13, 15 December 2011
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	What follows is a documented sample INDOCK file for [[DOCK 3.6]]. Many lines are required, lines starting with # are comments.		What follows is a documented sample INDOCK file for [[DOCK 3.6]]. Many lines are required, lines starting with # are comments.

	NOTE: do not under any circumstances use tab characters in this file.		'''NOTE: do not under any circumstances use tab characters in this file.'''

	Required first line:		Required first line:

2011-12-15T23:13:34Z

← Older revision		Revision as of 23:13, 15 December 2011
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	What follows is a documented sample INDOCK file for [[DOCK 3.6]]. Many lines are required, lines starting with # are comments.		What follows is a documented sample INDOCK file for [[DOCK 3.6]]. Many lines are required, lines starting with # are comments.

			NOTE: do not under any circumstances use tab characters in this file.

	Required first line:		Required first line:

2011-11-21T20:11:09Z

← Older revision		Revision as of 20:11, 21 November 2011
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	delphi_file ../../grids/rec+sph.phi		delphi_file ../../grids/rec+sph.phi
			delphi_nsize 179

	This controls the chemgrid file, which contains the van der Waals scoring for every coordinate (chem.vdw will be called) as well as the distance map grids that will be used for deciphering bumping (chem.bmp will be called).		This controls the chemgrid file, which contains the van der Waals scoring for every coordinate (chem.vdw will be called) as well as the distance map grids that will be used for deciphering bumping (chem.bmp will be called).

2011-10-26T20:45:32Z

change file date to match sphere change

2011-10-26T20:41:22Z

change match3 to match2

← Older revision		Revision as of 20:41, 26 October 2011
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	This is the path to the receptor matching spheres file. Most scripts make a set of directories and copy the INDOCK file into them, so this path sometimes has an extra set of "../" in it compared to what you might think. If you use [[DOCK Blaster]]. Generally, match3 has more spheres than match2, so produces more possible orientations. These spheres are matched to ligand spheres, generated from heavy atoms in the "rigid component" of each ligand. For more about the rigid component, see [[Flexibase Format]].		This is the path to the receptor matching spheres file. Most scripts make a set of directories and copy the INDOCK file into them, so this path sometimes has an extra set of "../" in it compared to what you might think. If you use [[DOCK Blaster]]. Generally, match3 has more spheres than match2, so produces more possible orientations. These spheres are matched to ligand spheres, generated from heavy atoms in the "rigid component" of each ligand. For more about the rigid component, see [[Flexibase Format]].

	receptor_sphere_file ../../sph/~~match3~~.sph		receptor_sphere_file ../../sph/match2.sph

	The next line is always 1, and is marked for deprecation.		The next line is always 1, and is marked for deprecation.

2011-10-19T23:39:58Z

← Older revision		Revision as of 23:39, 19 October 2011
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	#hydrogen_solvmap_file ../../grids/solvmap.sev.hydrogen		#hydrogen_solvmap_file ../../grids/solvmap.sev.hydrogen

	This is the phimap file used for electrostatic scoring. For a better understanding of this grid, see [[Visualizing delphi]].		This is the phimap file used for electrostatic scoring. For a better understanding of this grid, see [[Visualizing delphi]]. Sometimes this will change if you are using the new Qnifft Delphi maps, see [[Qnifft DOCK 3.6 conversion]].

	delphi_file ../../grids/rec+sph.phi		delphi_file ../../grids/rec+sph.phi

2011-10-17T01:43:10Z

note that remove_positive_solvation will be removed

← Older revision		Revision as of 01:43, 17 October 2011
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	check_clashes yes		check_clashes yes

	If set to yes, this removes the positive solvation from each ligand atom and spreads it evenly over the molecule. This is ~~not suggested~~.		If set to yes, this removes the positive solvation from each ligand atom and spreads it evenly over the molecule. This is deprecated because it does unexpected things to solvation, and will be removed entirely soon.

	remove_positive_solvation no		remove_positive_solvation no

2011-09-13T23:49:53Z

← Older revision		Revision as of 23:49, 13 September 2011
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	delphi_file ../../grids/rec+sph.phi		delphi_file ../../grids/rec+sph.phi

	This controls the chemgrid file, which contains the van der Waals scoring for every coordinate (chem.vdw will be called) as well as the distance map grids that will be used for ~~decipering~~ bumping (chem.bmp will be called).		This controls the chemgrid file, which contains the van der Waals scoring for every coordinate (chem.vdw will be called) as well as the distance map grids that will be used for deciphering bumping (chem.bmp will be called).

	chemgrid_file_prefix ../../grids/chem		chemgrid_file_prefix ../../grids/chem