ADL: regarding active site

Stefano Forli forli at
Fri Jun 12 20:17:12 PDT 2009

Dear Andreas, Davide, Joshi,

there is a little bit of misunderstanding related to procedures you described.

The position of the grid defines the tridimensional space in which the search is 
performed. The placement of the grid (i.e. the center) is relative to the protein 
coordinate system.

The best procedure would be to open ligand and protein as different objects and placing 
and resizing the grid via the AutoDockTools graphical user interface [1]:
-by manually tuning the parameters
-by center on atom, macromolecule or a ligand, if the location of the binding site is known.

The grid must be calculated on the protein structure without the ligand to be docked, and 
the grid size should be big enough to allow the arrangement of the ligand.

If the location of the binding site is not known, it's possible to perform a so called 
blind docking on the entire protein [2].

The docking calculation will try to find the best solution inside the pre-calculated grids.

The starting position of your ligand doesn't affect the calculation results.

The docking results should be inside the grid box. If none of them are in the box, 
something was not correctly set in the docking parameter file (the most frequent culprit 
is the "about" keyword).

If the docking results are inside the box but not in the experimental binding site (for 
that particular ligand) it could mean that search parameters used are not sufficient for 
sampling the search space.

The docking parameters can be defined as described in the AutoDockTools tutorial [1].

I hope this helps,



Davide Mercadante wrote:
> Dear Andreas,
> I also thought that probably autodock found some other position on the
> protein that would be more favourable for the docking of the ligand but this
> is strange and not acceptable:
> 1) Because some other studies of docking on very similar molecules (ligands)
> and the same enzyme confirm a strong affinity for these molecules in the
> active site and I expected the same...using another software (DOCK) the
> ligand is successful docked in the active site...
> 2) After the calculations the docked ligands are not in the box that I built
> to perform the calculation
> Something is definitively wrong. I just would like to understand what.
> Please, if you or anyone in the mail-list has any suggestion I will be happy
> to follow it.
> Cheers,
> Davide
> 2009/6/13 Kukol, Andreas <a.kukol at>
>> You need to save the ligand after moving, with the transformed coordinates.
>> It is possible that the ligand moved out of the binding site after docking,
>> in  that case AutoDock has found a more favorable position. It should,
>> however, not move outside the gridbox.
>> Andreas
>>> -----Original Message-----
>>> From: autodock-bounces at [mailto:autodock-bounces at]
>> On
>>> Behalf Of Davide Mercadante
>>> Sent: 12 June 2009 13:39
>>> To: autodock at
>>> Subject: Re: ADL: regarding active site
>>> Hi,
>>> I just did it using pmv given with autodock tools. However, the problem
>>> remains because after the calculations my ligand was not there anymore.
>>> how to position the ligand is explained here. Here is also written that
>> you
>>> can only move the ligand inside a grid. This means that I have to move
>> the
>>> ligand in the active site just after I create the grid box?
>>> How I can solve the problem?
>>> Thanks,
>>> Davide
>>> 2009/6/13 kaustubh <kaustubh.joshi at>
>>>> @Davide
>>>> How did you "Manually" positioned the ligand in the active site? Using
>>>> AutoDock?
>>>> If so please share!!
>>>> Davide Mercadante wrote:
>>>>> Dear Andreas,
>>>>> actually this happened also to me. I "manually" positioned my ligand
>> in
>>>>> the
>>>>> known active site of the enzyme and I centered the box on one atom of
>>> one
>>>>> of
>>>>> the residues that compose the active triad of my enzyme.
>>>>> However, after the calculations, I went to visualize the
>> conformations
>>>>> generated but the ligand just disappeared from the active site going
>>>>> somewhere else.
>>>>> Please, can you help me to understand why that happened and how can I
>>>>> solve
>>>>> the problem?
>>>>> Thanks infintely in advance for your help.
>>>>> Best Wishes,
>>>>> Davide
>>>>> Davide Mercadante - PhD student -
>>>>> Department of Chemistry
>>>>> Faculty of Science
>>>>> The University of Auckland
>>>>> Auckland 1142, New Zealand
>>>>> 2009/6/12 Kukol, Andreas <a.kukol at>
>>>>>> Use AutoDock Tools to centre the grid at a certain protein
>> (receptor)
>>>>>> atom
>>>>>> in the binding site and then adjust the position of the gridbox
>>>> manually,
>>>>>> such that the centre is centered above the binding site. This works
>>> very
>>>>>> well, but you need to do it visually.
>>>>>> Andreas
>>>>>> -----------------------
>>>>>>> -----Original Message-----
>>>>>>> From: autodock-bounces at
>>>>>> [mailto:autodock-bounces at]
>>>>>> On
>>>>>>> Behalf Of kaustubh
>>>>>>> Sent: 12 June 2009 11:09
>>>>>>> To: autodock at
>>>>>>> Subject: ADL: regarding active site
>>>>>>> How do we specify a known active site.
>>>>>>> The grid generation does not help doing so.
>>>>>>> While I specify to generate grid at the ligand position, it is
>>>>>> generated
>>>>>>> some where at vague position and also the docking take place some
>>>> where
>>>>>>> else, normally at the surface of the protein.
>>>>>>> This is not working out which ever way I try.
>>>>>>> Anybody their to help?
>>>>>>> --
>>>>>>> View this message in context:
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  Stefano Forli, PhD

  Research Associate
  Olson Molecular Graphics Laboratory
  Dept. Molecular Biology,  MB-5
  The Scripps Research Institute
  10550  North Torrey Pines Road
  La Jolla,  CA 92037-1000,  USA.

     tel: (858) 784-2055
     fax: (858) 784-2860
     email: forli at

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