DOCK 3.6 User Manual - Revision history

Khtang at 22:17, 2 January 2019

2019-01-02T22:17:51Z

← Older revision		Revision as of 22:17, 2 January 2019
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	[[DOCK 3.6]]		[[DOCK 3.6]]

	Here is the DOCK 3.5 manual from 1994: [http://wiki.bkslab.org/images/4/4e/Dock3_5refman.pdf DOCK 3.5 Manual]		Here is the DOCK 3.5 manual from 1994: [http://wiki.bkslab.org/images/4/4e/Dock3_5refman.pdf DOCK 3.5 Manual] {LINK NO LONGER WORKING}

	Note that DOCK 3.6 now uses Qnifft as a alternative to Delphi see [[Qnifft DOCK 3.6 conversion]] for dicussion of this change.		Note that DOCK 3.6 now uses Qnifft as a alternative to Delphi see [[Qnifft DOCK 3.6 conversion]] for dicussion of this change.

2012-10-08T20:02:01Z

27 revisions

← Older revision

Revision as of 20:02, 8 October 2012

2012-10-01T19:39:34Z

← Older revision		Revision as of 19:39, 1 October 2012
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	=DOCK 3 Scoring Function=		=DOCK 3 Scoring Function=
			{\| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:90%"
	solvmap_file ../.~~./grids/solvmap_sev~~		\|- style="background:lightgreen"
	delphi_file ~~../../grids/~~rec+sph2.qnifft.phi		! style="width 30%" !\|Parameter Name
	chemgrid_file_prefix ../../grids/chem		! style="width:70%" !\|Discription
	vdw_parameter_file ../../grids/vdw.parms.amb.mindock		\|-
	check_clashes yes		\| solvmap_file
	remove_positive_solvation no		\| solvmap_sev is . . .
	vdw_maximum 1.0e10		\|-
	electrostatic_scale 1.0		\|delphi_file
	vdw_scale 1.0		\| rec+sph2.qnifft.phi is assumed to be gerenerated with qnifft. If delphi grids are used modify delphi_nsize
			\|-
			\|delphi_nsize
			\| defult is 193. if using qnifft grids use defult. if using Delphi grids use 179. see [[Qnifft DOCK 3.6 conversion]] for more discution
			\|-
			\| chemgrid_file_prefix
			\| ../../grids/chem
			\|-
			\| vdw_parameter_file
			\| ../../grids/vdw.parms.amb.mindock
			\|-
			\| check_clashes
			\| yes
			\|-
			\| remove_positive_solvation
			\| no
			\|-
			\| vdw_maximum
			\| 1.0e10
			\|-
			\| electrostatic_scale
			\| 1.0
			\|-
			\| vdw_scale
			\| 1.0
			\|-

	[[Category:DOCK]]		[[Category:DOCK]]

2012-10-01T19:33:06Z

DOCK 3 Scoring Function

← Older revision		Revision as of 19:33, 1 October 2012
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	=DOCK 3 Scoring Function=		=DOCK 3 Scoring Function=

			solvmap_file ../../grids/solvmap_sev
			delphi_file ../../grids/rec+sph2.qnifft.phi
			chemgrid_file_prefix ../../grids/chem
			vdw_parameter_file ../../grids/vdw.parms.amb.mindock
			check_clashes yes
			remove_positive_solvation no
			vdw_maximum 1.0e10
			electrostatic_scale 1.0
			vdw_scale 1.0


	[[Category:DOCK]]		[[Category:DOCK]]

2012-10-01T19:32:28Z

History and Changes

← Older revision		Revision as of 19:32, 1 October 2012
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	Note that DOCK 3.6 now uses Qnifft as a alternative to Delphi see [[Qnifft DOCK 3.6 conversion]] for dicussion of this change.		Note that DOCK 3.6 now uses Qnifft as a alternative to Delphi see [[Qnifft DOCK 3.6 conversion]] for dicussion of this change.

			Using Qnifft grids with DOCK 3.5.54 may result in unresonably high electrostatic energies. So be aware of the DOCK version being used and the Electrostatic grids generation method.

	==Compilation==		==Compilation==

2012-10-01T19:30:11Z

History and Changes

← Older revision		Revision as of 19:30, 1 October 2012
Line 4:		Line 4:

	Here is the DOCK 3.5 manual from 1994: [http://wiki.bkslab.org/images/4/4e/Dock3_5refman.pdf DOCK 3.5 Manual]		Here is the DOCK 3.5 manual from 1994: [http://wiki.bkslab.org/images/4/4e/Dock3_5refman.pdf DOCK 3.5 Manual]

			Note that DOCK 3.6 now uses Qnifft as a alternative to Delphi see [[Qnifft DOCK 3.6 conversion]] for dicussion of this change.

	==Compilation==		==Compilation==

2012-09-25T17:07:49Z

Parameters

← Older revision		Revision as of 17:07, 25 September 2012
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	\|-		\|-
	\|cluster_numbers		\|cluster_numbers
	\|??		\|This has to do with the sphere clusters.
	\|-		\|-
	\|ligand_atom_file		\|ligand_atom_file

2012-09-25T17:05:18Z

SEARCH MODE

← Older revision		Revision as of 17:05, 25 September 2012
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	{\| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:90%"		{\| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:90%"
	\|- style="background:~~lightred~~"		\|- style="background:red"
	! style="width 30%" !\|Parameter Name		! style="width 30%" !\|Parameter Name
	! style="width:70%" !\|Discription		! style="width:70%" !\|Discription

2012-09-25T17:04:55Z

SEARCH MODE

← Older revision		Revision as of 17:04, 25 September 2012
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	{\| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:90%"		{\| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:90%"
	\|- style="background:~~lightgreen~~"		\|- style="background:lightred"
	! style="width 30%" !\|Parameter Name		! style="width 30%" !\|Parameter Name
	! style="width:70%" !\|Discription		! style="width:70%" !\|Discription

2012-09-25T17:04:06Z

SEARCH MODE

← Older revision		Revision as of 17:04, 25 September 2012
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	\|-		\|-
	\| mode		\| mode
	\| This parameter has be deprecated. Only the "search" mode is curently used. the "single" mode, which ~~aloud~~ multiple ligand conformations to be saved, was broken and was removed from DOCK 3.6. This fuctionality is in version 3.5 (Mpose binary [[MPose]]). The ligand clustering [[Dock Ligand Clustering]] code also alows for multiple conformations to be saved.		\| This parameter has be deprecated. Only the "search" mode is curently used. the "single" mode, which alowed multiple ligand conformations to be saved, was broken and was removed from DOCK 3.6. This fuctionality is in version 3.5 (Mpose binary [[MPose]]). The ligand clustering [[Dock Ligand Clustering]] code also alows for multiple conformations to be saved.
	\|-		\|-