[Dock-fans] Write multiple conformations during parallel processing

Cen Gao cengao at gmail.com
Tue Jul 13 09:13:53 PDT 2010

Dear Dock fans:

May I ask is it possible for DOCK to write out the top N conformers for each
molecule it processed during the parallel docking run? The manual states
that this feature is only available to serial version of DOCK to "protect
against filling up the disk", as "in conformer.mol2, the number of molecules
in the output file will be equal to the database size * the number of
anchors per molecule * the number of conformations that pass the final
pruning stage * the number of conformers per cycle."

But if I understand it right, this conformer number should not be that huge
as it is something we can control using the keyword "num_scored_conformer"
(in the case of primary_score only), right?  As long as I set this keyword
to a smaller value, say 3 or 5, it will only write 3 or 5 poses per
molecule, which will not be a problem in case of the file size. Did I miss
something here?


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