[Dock-fans] orientations and conformations

Ravinder Abrol abrol at wag.caltech.edu
Mon Jun 22 04:17:32 PDT 2009


Hi,
I am running Dock 6.2 using a flexible ligand for generating many poses to use 
with our own scoring functions and I want to control the number of 
conformations that are generated at the end. I am only using bumps and 
clash_overlap to eliminate poses. I understand the anchor and grow approach 
but how I can control it with the available input options available is not 
clear to me. I am providing below results of two runs along with partial 
input used to generate them. If you can help me make sense of the numbers, 
that will greatly help.

>Run1
Input1:
max_orientations  1000
pruning_use_clustering  yes
pruning_max_orients  100
pruning_clustering_cutoff  1000
Output1:
 Anchors: 1
 Orientations:  492
 Conformations:  975

>Run2
Input2:
max_orientations  1000
pruning_use_clustering  yes
pruning_max_orients  1000
pruning_clustering_cutoff  1000
Output2:
 Anchors:  1
 Orientations:  492
 Conformations:  1023

Does 492 mean that it found 492 possible placements of the anchor?
If yes, then how is pruning_max_orients and pruning_clustering_cutoff used?
I don't understand that in Run2 I specified 1000 for 
pruning_clustering_cutoff, but at the end I got 1023 conformations.
In other words, is there a way to control the final number of conformations 
that are generated?

Thanks.
Ravi



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