Dock Ligand Clustering - Revision history

Therese: 9 revisions

2012-10-08T20:11:53Z

9 revisions

← Older revision

Revision as of 20:11, 8 October 2012

Mkorcz at 19:59, 8 February 2012

2012-02-08T19:59:14Z

← Older revision		Revision as of 19:59, 8 February 2012
Line 49:		Line 49:

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

			-----

			Currently (Feb 2012) if you have problems running the above script you may need a distmap file in your grids directory (just type 'distmap' in the grids directory and it should be created automatically, this will not be used in the calculations but it is something that dock needs to read in at this time) also add the line into INDOCK

			###############################################################################
			# SCORING
			#
			distmap_file ../grids/distmap

			You may also need to comment the random seed line out of the INDOCK file

			###############################################################################
			################## DOCK 3.5 INPUT PARAMETERS 2011/10/26 #######################
			###############################################################################
			###############################################################################
			# INPUT/OUTPUT
			#
			#random_seed 777

Rgc at 23:34, 6 February 2012

2012-02-06T23:34:16Z

← Older revision		Revision as of 23:34, 6 February 2012
Line 42:		Line 42:
	~xyz/dockenv/bin/Linux/ligandclustering/		~xyz/dockenv/bin/Linux/ligandclustering/

	Bonus: A version compiled with nsize=193 for use with Qnifft [[~~http://wiki.bkslab.org/index.php/~~Qnifft_DOCK_3.6_conversion]] is in		Bonus: A version compiled with nsize=193 for use with Qnifft [[Qnifft_DOCK_3.6_conversion]] is in

	~xyz/dockenv/bin/Linux/ligandclustering-qnifft/		~xyz/dockenv/bin/Linux/ligandclustering-qnifft/

Rgc at 23:34, 6 February 2012

2012-02-06T23:34:02Z

← Older revision		Revision as of 23:34, 6 February 2012
Line 41:		Line 41:

	~xyz/dockenv/bin/Linux/ligandclustering/		~xyz/dockenv/bin/Linux/ligandclustering/

			Bonus: A version compiled with nsize=193 for use with Qnifft [[http://wiki.bkslab.org/index.php/Qnifft_DOCK_3.6_conversion]] is in

			~xyz/dockenv/bin/Linux/ligandclustering-qnifft/

			Or where ~xyz/dockenv is your $DOCK_BASE

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

Rgc at 23:38, 14 November 2011

2011-11-14T23:38:39Z

← Older revision		Revision as of 23:38, 14 November 2011
Line 41:		Line 41:

	~xyz/dockenv/bin/Linux/ligandclustering/		~xyz/dockenv/bin/Linux/ligandclustering/

			[[Category:DOCK]]

Rgc at 21:04, 9 November 2011

2011-11-09T21:04:14Z

New page

DOCK 3.6 Ligand Clustering

* branch of [[DOCK_3.6]]
* Contributed by Niu Huang's lab
* Currently in the niu-nibs-clustering branch, ready for use
* Replacement for single mode
* Example INDOCK file parameters, add to your current INDOCK file

#
################################################################################
# POSE_CLUSTERING
#
pose_clustering yes
# "yes/no" General switch of pose clustering (default: no)
pose_clustering_detail no
# "yes/no" Switch of print out detail infomation (default: no)
pose_clustering_method 0
# 0---------Write all the poses
# 1---------Clustering method based on KGS penalty function
# 2---------Clustering method based on ratio of RANK and RMSD
pose_clustering_cutoff 1.1
# pre-determined variable for clustering cutoff
# In method 0, the cutoff is unused.
# In method 1, the cutoff is unused.
# In method 2, the cutoff is Nc.
################################################################################
# cutoff in pose_clustering for saving resource
#pose_clustering_RMSD_cutoff
#pose_clustering_energy_cutoff no
pose_clus_inputno_cutoff 0
# number: input number cutoff; 0: no; -1: rotatable bond based (NA)
# number of poses to be clustered according to energy rank
# for method 0, it is also used.
pose_clus_outputno_cutoff 0
# number: output number cutoff; 0: no
# number of clustered poses being written out according to energy rank
# for method 0, it is also used.
################################################################################

Currently installed in

~xyz/dockenv/bin/Linux/ligandclustering/

Rgc at 23:02, 17 August 2011

2011-08-17T23:02:10Z

← Older revision		Revision as of 23:02, 17 August 2011
Line 36:		Line 36:
	# for method 0, it is also used.		# for method 0, it is also used.
	################################################################################		################################################################################

			Currently installed in

			~xyz/dockenv/bin/Linux/ligandclustering/

Rgc at 21:42, 21 July 2011

2011-07-21T21:42:32Z

← Older revision		Revision as of 21:42, 21 July 2011
Line 4:		Line 4:
	* Currently in the niu-nibs-clustering branch, ready for use		* Currently in the niu-nibs-clustering branch, ready for use
	* Replacement for single mode		* Replacement for single mode
	* Example INDOCK file parameters		* Example INDOCK file parameters, add to your current INDOCK file

	#		#

Rgc: first version

2011-07-21T21:42:14Z

first version

New page

DOCK 3.6 Ligand Clustering

* Contributed by Nia Huang's lab
* Currently in the niu-nibs-clustering branch, ready for use
* Replacement for single mode
* Example INDOCK file parameters

#
################################################################################
# POSE_CLUSTERING
#
pose_clustering yes
# "yes/no" General switch of pose clustering (default: no)
pose_clustering_detail no
# "yes/no" Switch of print out detail infomation (default: no)
pose_clustering_method 0
# 0---------Write all the poses
# 1---------Clustering method based on KGS penalty function
# 2---------Clustering method based on ratio of RANK and RMSD
pose_clustering_cutoff 1.1
# pre-determined variable for clustering cutoff
# In method 0, the cutoff is unused.
# In method 1, the cutoff is unused.
# In method 2, the cutoff is Nc.
################################################################################
# cutoff in pose_clustering for saving resource
#pose_clustering_RMSD_cutoff
#pose_clustering_energy_cutoff no
pose_clus_inputno_cutoff 0
# number: input number cutoff; 0: no; -1: rotatable bond based (NA)
# number of poses to be clustered according to energy rank
# for method 0, it is also used.
pose_clus_outputno_cutoff 0
# number: output number cutoff; 0: no
# number of clustered poses being written out according to energy rank
# for method 0, it is also used.
################################################################################