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

Jonathan Gough jonathan.d.gough at gmail.com
Wed Mar 23 07:22:31 PDT 2016

Hi Dwight,

Not exactly. At the moment, I am simply trying to reproduce the docking
experiment for pygm. This is one of a few receptors in DUD-e that has an
explicit water present in the receptor.pdb.


In general, we are looking at explicit waters and water structure and would
like to be able to use dock to run experiments with an explicit water
(hence trying to reproduce pygm to make sure we know what we are doing).

Any insight would be appreciated,

On Wed, Mar 23, 2016 at 10:16 AM, Dwight McGee <dwight.mcgee at gmail.com>

> Hi Jonathan,
> Pertaining to question #2. Are you trying to identify ligands that make a
> specific water mediated interaction with the receptor?
> Best,
> Dwight
> On Tue, Mar 22, 2016 at 7:17 PM, Jonathan Gough <
> jonathan.d.gough at gmail.com> wrote:
>> 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
> them."
>                 Albert Einstein
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