ADL: regarding active site

kaustubh kaustubh.joshi at
Fri Jun 12 05:06:12 PDT 2009

Going bit deeper with the query:
1)I was wondering whether we should retain the native ligand in protein
structure converting it to pdbqt.
Like in DS or Schrodinger  the active site generated considering native
ligand at the center. AutoDock doesnt give such an option.
2) I tried few many things while generating the grid ( bothways : keeping
native ligand as well as deleting it)
i)opted for grid with central atom of the native ligand as the center of
ii) opted for an atom in the residue closet to the native ligand. Here I
deleted the ligand.
iii)Selecting center of protein  as center of grid with full expansion of
grid cube.(It compasses whole of the protein).
iv) Manually changing the grid center to the center of native or nearest
v) Manually changed the grid center in gpf dile as well as ligand center in
dpf file with expected center. 
One more observation as well as query is when we open the protein and the
ligand structure in ADT, the ligand occupies some random space around the
protein. Is their any way to bring this ligand inside the proposed active
site ? 

thanks Andreas!  for the advise. Although I tried that way earlier, but will
try to play with it again. May be it will click and I get the clue! If any
other way known, kindly let me know.

Kukol, Andreas wrote:
> 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?
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