[Dock-fans] Write multiple conformations during parallel processing

Sudipto Mukherjee sudmukh at yahoo.com
Thu Jul 15 14:21:23 PDT 2010

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. 

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?



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