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

Jonathan Gough jonathan.d.gough at gmail.com
Wed Mar 23 09:16:17 PDT 2016


Very helpful, Trent. Thank you!

1.  Do you know which systems in DUDE are prepared for dock6? (or can you
let me know what tell-tale signs/files to look for and I can go fishing
myself?)

2. Where would be the best place to look to make sure I have the
appropriate  partial charges and atom types for water?

Presently,water is in my mol2. The anotations in said receptor.mol2 file
are:
.
.
.
   3776 OW         34.0560   32.5760   31.6400 O.t3p   379 WAT   -0.8340
   3777 HW1        34.7800   33.2250   31.7360 H.t3p   379 WAT    0.4170
   3778 HW2        34.3540   31.8730   31.0610 H.t3p   379 WAT    0.4170
.
.
.

   379 WAT  3776 RESIDUE           4 A     WAT     0 ROOT



On Wed, Mar 23, 2016 at 12:06 PM, Trent E. Balius <tbalius at aol.com> wrote:

> Hi Jonathan,
>
> Question1.
>   A subset of the systems of the DUDE systems are distributed with
> SB2010/SB2012
>   which are prepared for DOCK6
>   Otherwise, you will need to prepare the receptors yourself,
>   I would suggest using Chimera and its dock prep tool to help you
> prepare the receptors.
>   I would also suggest using the mol2 file distributed with DUDE (audoDUDE
> is for DOCK3.7):
>      http://dude.docking.org/
>      here are the mol2 files:
>      http://dude.docking.org/targets/aa2ar/actives_final.mol2.gz
>      http://dude.docking.org/targets/aa2ar/decoys_final.mol2.gz
> Question2:
>   Including waters is possible in DOCK3.7 but a little tricky:
>   see the following:
>   http://wiki.bkslab.org/index.php/DOCK_3.7_tutorial_%28Anat%29
>   you will need to use "blastermaster.py -v --addNOhydrogensflag"
>
>   For dock6 it is a little easier,  you just need to make sure that the
> water
>   is in the mol2 file (and it has the right partial charges and atom type
> for grid to run properly).
>
> I hope that this helps,
>
> Trent
>
> ======================================
> Trent E. Balius, PhD
> Postdoc, Shoichet Lab,
> Dept. Pharm. Chem., UCSF
> Phone: (415) 514-4253
> URL: http://docking.org/~tbalius
> ======================================
>
>
> -----Original Message-----
> From: Jonathan Gough <jonathan.d.gough at gmail.com>
> To: Dwight McGee <dwight.mcgee at gmail.com>
> Cc: dock-fans <dock-fans at docking.org>
> Sent: Wed, Mar 23, 2016 7:28 am
> Subject: Re: [Dock-fans] auto-DUD-e and explicit water -- Dock 6.7
>
> 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.
>
> http://dude.docking.org/targets/pygm
>
> 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,
> Jonathan
>
> On Wed, Mar 23, 2016 at 10:16 AM, Dwight McGee <dwight.mcgee at gmail.com>
> wrote:
>
>> 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
>>>
>>> _______________________________________________
>>> Dock-fans mailing list
>>> Dock-fans at docking.org
>>> http://mailman.docking.org/mailman/listinfo/dock-fans
>>>
>>>
>>
>>
>> --
>> 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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