Dock Ligand Clustering

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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/

Bonus: A version compiled with nsize=193 for use with Qnifft Qnifft_DOCK_3.6_conversion is in

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

Or where ~xyz/dockenv is your $DOCK_BASE


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