[Dock-fans] auto-DUD-e and explicit water -- Dock 6.7

Dwight McGee dwight.mcgee at gmail.com
Wed Mar 23 07:16:24 PDT 2016

Hi Jonathan,

Pertaining to question #2. Are you trying to identify ligands that make a
specific water mediated interaction with the receptor?


On Tue, Mar 22, 2016 at 7:17 PM, Jonathan Gough <jonathan.d.gough at gmail.com>

> Hi all,
> 2 questions -
> 1. I was wondering if it is possible to use the files for auto-DUD-E in
> testing for Dock 6.7. It seems as if everything is set up for 3.7, but not
> for 6.7.
> Related to that, I tried using basic steps in the tutorials to reproduce
> the binding of the x-ray crystal ligand from pygm (in the DUD-E) using the
> ligand.mol2 and the receptor.pdb from http://dude.docking.org/
> unfortunately, the generated poses were very far from expected.
> 2. when prepping the grid scoring function (or the pdb/mol2), is there
> something special that I need to do to ensure that the explicit water is
> treated correctly or to make sure that the water parameters are included?
> Thanks,
> Jonathan
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T. Dwight McGee Jr.

dwight.mcgee at gmail.com

"Problems cannot be solved at the same level of awareness that created
                Albert Einstein
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