[Dock-fans] auto-DUD-e and explicit water -- Dock 6.7
jonathan.d.gough at gmail.com
Tue Mar 22 16:17:45 PDT 2016
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
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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