[Dock-fans] ranked.mol2

Sudipto Mukherjee sudmukh at yahoo.com
Tue Nov 6 08:20:14 PST 2007


Imtiaz,

You could run dock with 'num_scored_conformers_written' set to a high number (e.g. 500) with clustering turned on. Then you can select the top 20 or so clusterheads from the mol2 file using a script, or by running dock again and using max_ligands=20.
 
Regards
Sudipto Mukherjee
Graduate Student, Robert C. Rizzo Lab
Dept. of Applied Math & Statistics, Stony Brook University

----- Original Message ----
From: Imtiaz M. <biobrain at gmail.com>
To: dock-fans at docking.org
Sent: Monday, November 5, 2007 8:20:14 AM
Subject: [Dock-fans] ranked.mol2


Dear All,

I am using the following options

num_scored_conformers_written                        20
cluster_conformations                                        yes
cluster_rmsd_threshold                                      2.0
rank_ligands                                                       yes
max_ranked_ligands                                           500


Please tell me how I can get clusters of the different possible
solutions. How I can select Top 20 solution for my docking experiment.
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