Dock Ligand Clustering: Difference between revisions
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DOCK 3.6 Ligand Clustering | DOCK 3.6 Ligand Clustering | ||
* Contributed by | * branch of [[DOCK_3.6]] | ||
* Contributed by Niu Huang's lab | |||
* 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 |
Revision as of 21:04, 9 November 2011
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/