[Dock-fans] Write multiple conformations during parallel processing
sudmukh at yahoo.com
Fri Jul 16 10:04:07 PDT 2010
A maximum of 3 docked conformers will be written to prefix_scored.mol2
Nothing will be written to prefix_confomer.mol2 with write_conformations set to
In your case, what is happening is that after scoring, pruning and clustering,
only one viable docked conformation remains. You will get up to 3 conformations
in prefix_scored.mol2 if you keep trying with different ligands. I suggest that
try this with a small database of 1000 ligands instead of just docking in one
molecule. You should that many of them will have 2 or more conformers in the
For your reference, here is the dock input file I used to verify this:
Trent E. Balius
Graduate Student, Robert C. Rizzo Lab
Dept. of Applied Math & Statistics, Stony Brook University
From: Cen Gao <cengao at gmail.com>
To: Sudipto Mukherjee <sudmukh at yahoo.com>
Cc: Dock-fans at mailman.docking.org
Sent: Thu, July 15, 2010 6:03:42 PM
Subject: Re: [Dock-fans] Write multiple conformations during parallel
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
On Thu, Jul 15, 2010 at 5:21 PM, Sudipto Mukherjee <sudmukh at yahoo.com> wrote:
>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.
>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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