DOCK 3.7 tutorial (Anat) - Revision history

Matthew O'Meara: fix typo art -> tart

2020-08-19T16:46:11Z

fix typo art -> tart

← Older revision		Revision as of 16:46, 19 August 2020
Line 78:		Line 78:
	Edit RSK2-tart/amb.crg.oxt to reflect the same changes		Edit RSK2-tart/amb.crg.oxt to reflect the same changes
	Now all that's left is to run the protein preparation script (blastermaster.py) with the modified parameter files, and without re-protonating the protein:		Now all that's left is to run the protein preparation script (blastermaster.py) with the modified parameter files, and without re-protonating the protein:
	blastermaster.py --addNOhydrogensflag --chargeFile=/path/to/RSK2-tart/amb.crg.oxt --vdwprottable=/path/to/RSK2-~~art~~/prot.table.ambcrg.ambH		blastermaster.py --addNOhydrogensflag --chargeFile=/path/to/RSK2-tart/amb.crg.oxt --vdwprottable=/path/to/RSK2-tart/prot.table.ambcrg.ambH
	the path for the prot.table.amb.crg.ambH and amb.crg.oxt files should be in the up directory and NOT in the ‘working’ directory.		the path for the prot.table.amb.crg.ambH and amb.crg.oxt files should be in the up directory and NOT in the ‘working’ directory.
	When the preparation is done, your protein should be "Tarted". You can proceed to docking.		When the preparation is done, your protein should be "Tarted". You can proceed to docking.

2017-06-12T16:11:01Z

Set docking directories

← Older revision		Revision as of 16:11, 12 June 2017
Line 33:		Line 33:
	ln -s ../dockfiles/ .		ln -s ../dockfiles/ .

	python ${DOCKBASE}/docking/setup/setup_db2_zinc15_file_number.py ./ vs_frag /path/to/ZINC-downloader-3D-db2.gz.database_index ~~500~~ count		python ${DOCKBASE}/docking/setup/setup_db2_zinc15_file_number.py ./ vs_frag /path/to/ZINC-downloader-3D-db2.gz.database_index 1000 count

	See the this page: [[Trent_scripts]]		See the this page: [[Trent_scripts]]

2017-06-12T16:09:49Z

Set docking directories

← Older revision		Revision as of 16:09, 12 June 2017
Line 33:		Line 33:
	ln -s ../dockfiles/ .		ln -s ../dockfiles/ .

	python ${DOCKBASE}/docking/setup/setup_db2_zinc15_file_number.py ./ vs_frag /~~nfs~~/~~work~~/~~tbalius/database_ph4/frags~~.~~txt~~ 500 count		python ${DOCKBASE}/docking/setup/setup_db2_zinc15_file_number.py ./ vs_frag /path/to/ZINC-downloader-3D-db2.gz.database_index 500 count

	See the this page: [[Trent_scripts]]		See the this page: [[Trent_scripts]]

2017-06-12T16:08:13Z

Set docking directories

← Older revision		Revision as of 16:08, 12 June 2017
Line 33:		Line 33:
	ln -s ../dockfiles/ .		ln -s ../dockfiles/ .

	python ${DOCKBASE}/docking/setup/setup_db2_zinc15_file_number.py ./ vs_frag /nfs/work/tbalius/database_ph4/frags.txt 500 count		python ${DOCKBASE}/docking/setup/setup_db2_zinc15_file_number.py ./ vs_frag /nfs/work/tbalius/database_ph4/frags.txt 500 count

	See the this page: [[Trent_scripts]]		See the this page: [[Trent_scripts]]

2017-06-12T16:07:01Z

ligand prep

← Older revision		Revision as of 16:07, 12 June 2017
Line 18:		Line 18:

	* Make sure that there are no ^M in the smiles input file - use dos2unix [file name] command remove them.		* Make sure that there are no ^M in the smiles input file - use dos2unix [file name] command remove them.

			===Set docking directories===
	* This is for running a virtual screen on a ZINC subset, thing can be in different paths.		* This is for running a virtual screen on a ZINC subset, thing can be in different paths.
	* Input file should contain a db2 file on each line with full path.		* Input file should contain a db2 file on each line with full path.
Line 30:		Line 32:
	cd Frag/		cd Frag/
	ln -s ../dockfiles/ .		ln -s ../dockfiles/ .
	~~setup_db2_zinc15_file~~.py . ~~fragments database_index~~
			python ${DOCKBASE}/docking/setup/setup_db2_zinc15_file_number.py ./ vs_frag /nfs/work/tbalius/database_ph4/frags.txt 500 count

	See the this page: [[Trent_scripts]]		See the this page: [[Trent_scripts]]

2016-11-02T22:21:12Z

Using modified(existing) delphi spheres:

← Older revision		Revision as of 22:21, 2 November 2016
Line 93:		Line 93:

	=== Using modified(existing) delphi spheres: ===		=== Using modified(existing) delphi spheres: ===
	[[using thin spheres in DOCK3.7]]		[[using thin spheres in DOCK3.7]]

	blastermaster.py --useExistingLowDielectricSphflag --addNOhydrogensflag		blastermaster.py --useExistingLowDielectricSphflag --addNOhydrogensflag

2016-11-02T22:20:52Z

← Older revision		Revision as of 22:20, 2 November 2016
Line 93:		Line 93:

	=== Using modified(existing) delphi spheres: ===		=== Using modified(existing) delphi spheres: ===
			[[using thin spheres in DOCK3.7]]

	blastermaster.py --useExistingLowDielectricSphflag --addNOhydrogensflag		blastermaster.py --useExistingLowDielectricSphflag --addNOhydrogensflag

2016-04-06T20:04:06Z

ligand prep

← Older revision		Revision as of 20:04, 6 April 2016
Line 20:		Line 20:
	* This is for running a virtual screen on a ZINC subset, thing can be in different paths.		* This is for running a virtual screen on a ZINC subset, thing can be in different paths.
	* Input file should contain a db2 file on each line with full path.		* Input file should contain a db2 file on each line with full path.
	* This file may be downloaded from the zinc webpage: 'http://zinc15.docking.org/tranches/home/'		* This file may be downloaded from the zinc webpage: '[http://zinc15.docking.org/tranches/home http://zinc15.docking.org/tranches/home]'

	setup_db2_zinc15_file.py '$DOCKBASE/docking/setup/setup_db2_zinc15_file.py'		setup_db2_zinc15_file.py '$DOCKBASE/docking/setup/setup_db2_zinc15_file.py'

2016-04-06T20:02:07Z

ligand prep

← Older revision		Revision as of 20:02, 6 April 2016
Line 20:		Line 20:
	* This is for running a virtual screen on a ZINC subset, thing can be in different paths.		* This is for running a virtual screen on a ZINC subset, thing can be in different paths.
	* Input file should contain a db2 file on each line with full path.		* Input file should contain a db2 file on each line with full path.
	* This file may be downloaded from the zinc webpage: 'http://zinc15.docking.org/tranches/~~build~~/#'		* This file may be downloaded from the zinc webpage: 'http://zinc15.docking.org/tranches/home/'

	setup_db2_zinc15_file.py '$DOCKBASE/docking/setup/setup_db2_zinc15_file.py'		setup_db2_zinc15_file.py '$DOCKBASE/docking/setup/setup_db2_zinc15_file.py'

2016-01-26T16:51:58Z

Using modified(existing) matching spheres:

← Older revision		Revision as of 16:51, 26 January 2016
Line 90:		Line 90:
	blastermaster.py --useExistingMatchingSphflag		blastermaster.py --useExistingMatchingSphflag

	~~note~~ that this is a newer ~~fetcher~~ and is ~~not~~ included		Note that this is a newer feature and is included in DOCK-3.7-beta3 release and later versions.

	=== Using modified(existing) delphi spheres: ===		=== Using modified(existing) delphi spheres: ===