Tutorial on running DOCK3.7 with GIST - Revision history

TBalius: /* Prepare system for docking */

2017-11-16T01:31:58Z

Prepare system for docking

← Older revision		Revision as of 01:31, 16 November 2017
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	cd $workdir		cd $workdir
	$DOCKBASE/proteins/blastermaster/blastermaster.py --addhOptions=" -HIS -FLIPs " --addhDict="$pramdir/reduce_wwPDB_het_dict_mod.txt" --chargeFile="$pramdir/amb_mod.crg.oxt" --vdwprottable="$pramdir/prot_mod.table.ambcrg.ambH" -v		$DOCKBASE/proteins/blastermaster/blastermaster.py --addhOptions=" -HIS -FLIPs " --addhDict="$pramdir/reduce_wwPDB_het_dict_mod.txt" --chargeFile="$pramdir/amb_mod.crg.oxt" --vdwprottable="$pramdir/prot_mod.table.ambcrg.ambH" -v
			# modify to the following if there is no cofactor
			# $DOCKBASE/proteins/blastermaster/blastermaster.py --addhOptions=" -HIS -FLIPs " -v
	EOF		EOF

2017-11-16T01:30:43Z

Get ligand databases

← Older revision		Revision as of 01:30, 16 November 2017
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	For the CcP ligands download the dock-ready databases from here:		For the CcP ligands download the dock-ready databases from here:
	wget http://docking.org/~tbalius/code/waterpaper2017/CcP-ga_ph4_justdb2.tar.gz		wget http://docking.org/~tbalius/code/waterpaper2017/CcP-ga_ph4_justdb2.tar.gz
			wget http://docking.org/~tbalius/code/waterpaper2017/for011.dockprep_parm_files.tar.gz
	tar -xzvf CcP-ga_ph4_justdb2.tar.gz		tar -xzvf CcP-ga_ph4_justdb2.tar.gz
			tar -xzvf for011.dockprep_parm_files.tar.gz

	You can download other databases from the autodude web page:		You can download other databases from the autodude web page:

2017-04-19T16:52:23Z

docking

← Older revision		Revision as of 16:52, 19 April 2017
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	# matching_spheres.sph		# matching_spheres.sph

	== ~~docking~~ ==		== Docking ==
	Create and apply a patch to the INDOCK file (012.dock.gistpatch.csh).		Create and apply a patch to the INDOCK file (012.dock.gistpatch.csh).

2017-04-19T16:51:20Z

prepare system for docking

← Older revision		Revision as of 16:51, 19 April 2017
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	== ~~prepare~~ system for docking ==		== Get ligand databases ==

			For the CcP ligands download the dock-ready databases from here:
			wget http://docking.org/~tbalius/code/waterpaper2017/CcP-ga_ph4_justdb2.tar.gz
			tar -xzvf CcP-ga_ph4_justdb2.tar.gz

			You can download other databases from the autodude web page:
			[[DOCK_3.7_2015/04/15_abl1_Tutorial#set_up_directories_and_get_databases]]

			== Prepare system for docking ==
	Write the following script (011.dock.blastermaster.csh) to run blastermaster.		Write the following script (011.dock.blastermaster.csh) to run blastermaster.
	#!/bin/csh		#!/bin/csh

2017-04-18T21:00:23Z

enrichment

@@ Line 285: / Line 285: @@
   end # pdbname
-== enrichment ==
+== Enrichment ==
 == prepare system for docking (flex) ==

2017-04-17T23:23:59Z

docking

2017-04-17T23:18:02Z

← Older revision		Revision as of 23:18, 17 April 2017
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	This tutorial assumes that you have already completed the MD tutorial [[Tutorial on running Molecular Dynamics for GIST grid generation with scripts]].		This tutorial assumes that you have already completed the MD tutorial [[Tutorial on running Molecular Dynamics for GIST grid generation with scripts]].

	# use ~~the align~~ the receptor and ligand to the MD frame.		# use the receptor and ligand the align to the MD frame.
	# prepare the receptor for docking using blastermaster. Flexible receptor docking is approximated by docking to 16 states.		# prepare the receptor for docking using blastermaster. Flexible receptor docking is approximated by docking to 16 states.
	# modify the INDOCK file.		# modify the INDOCK file.

2017-04-17T20:32:25Z

prepare system for docking (flex)

@@ Line 130: / Line 130: @@
   # we have already aligned the ligand previously.
   ln -s $mountdir/gist/007align_to_md/lig_aligned.pdb .
+ mkdir -p $workdir
 == docking (flex) ==
 == enrichment (flex) ==

2017-04-17T19:17:14Z

@@ Line 4: / Line 4: @@
 here are more GIST related tutorials: [[ DOCK_3.7_with_GIST_tutorials]]
-This tutorial assumes that you have already completed the MD tutorial [[Tutorial on running Molecular Dynamics for GIST grid generation]].
+This tutorial assumes that you have already completed the MD tutorial [[Tutorial on running Molecular Dynamics for GIST grid generation with scripts]].
 # use the align the receptor and ligand to the MD frame.
@@ Line 12: / Line 12: @@
 # Dock ligand and decoy databases and perform enrichment analysis
 # perform enrichment analyis

2017-04-17T16:55:39Z

← Older revision		Revision as of 16:55, 17 April 2017
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	Tutorial by Trent Balius (2017/01/30).		Tutorial by Trent Balius (2017/01/30).

			here are more GIST related tutorials: [[ DOCK_3.7_with_GIST_tutorials]]

	This tutorial assumes that you have already completed the MD tutorial [[Tutorial on running Molecular Dynamics for GIST grid generation]].		This tutorial assumes that you have already completed the MD tutorial [[Tutorial on running Molecular Dynamics for GIST grid generation]].