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

Jonathan Gough jonathan.d.gough at gmail.com
Tue Mar 22 16:17:45 PDT 2016

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?

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