[Dock-fans] orientations and conformations
abrol at wag.caltech.edu
Mon Jun 22 04:17:32 PDT 2009
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.
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?
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