[Dock-fans] Write multiple conformations during parallel processing

Cen Gao cengao at gmail.com
Thu Jul 15 15:03:42 PDT 2010

Hi Sudipto:

Thanks for the email. I have tried to set  "num_scored_conformer" to 3 and
"write_conformations" to No before, but it still generated only one pose per
molecule to prefix_scored.mol2, while never wrote anything to
prefix_confomer.mol2. May I ask whether this setting works differently on
your version of DOCK?  (I am using DOCK6.4, compiled with GCC4.1)  Or are
there any parameters I should set?

If I set write_conformations to yes, it was able to write 1 pose to
prefix_scored.mol2 and 3 poses per molecule into prefix_confomer.mol2 as
expected. But again it works in serial version of DOCK only, but refuses to
run in parallel.



On Thu, Jul 15, 2010 at 5:21 PM, Sudipto Mukherjee <sudmukh at yahoo.com>wrote:

> Hi Cen,
> As you mentioned in your email, the "num_scored_conformer" is the parameter
> you want to use.
> Set this to 3 as you wish.
> Set "write_conformations" as no. By default this is yes. The naming
> convention is a bit confusing here, I admit. The write_conformations
> parameter writes out partial conformers in a separate conformers.mol2
> Setting this parameter to yes is what geenrates the ERROR about filling up
> the disk during mpi runs.
> Now you should have a maximum of 3 conformers for each molecule screened.
> Regards
> Sudipto Mukherjee
> Graduate Student, Robert C. Rizzo Lab
> Dept. of Applied Math & Statistics, Stony Brook University
> ------------------------------
> *From:* Cen Gao <cengao at gmail.com>
> *To:* Dock-fans at mailman.docking.org
> *Sent:* Tue, July 13, 2010 12:13:53 PM
> *Subject:* [Dock-fans] Write multiple conformations during parallel
> processing
> 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?
> Thanks
> Cen
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