Subject: Re: CCL:autodock -active site-summary

From: Johanna Mazlo <[email-masked]>
Date: Fri, 27 Jul 2001 17:06:38 -0500 (CDT)

Dear CCL group,

Thank you all for help regarding searching only the active site when
docking the ligand to the receptor in Autodock.  As I promised, below are
the responses.  

Johanna Mazlo
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You can do that by precisely tailoring the grid size as to
include only the region of interest. Start from a receptor-
ligand complex (ie the ligand bound to the active site).
mkgdf3 build a grid centered on the ligand (gridcenter keyword
on your gpf file) that will be explored by the ligand during the
search. if the grid fits the active site, your ligand will only
move within that site. you have to play with npts keyword in the
gpf file (number of gridpoint per direction, only even number!)
in order to size the grid exactly. a useful program to visualise
the extents of the grid is avs

regards,

fabrizio
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I read your mail regarding autodock.  I'm using autodock as well for my
work. I'm using a crystal structure of my protein-ligand and I specify the
active site according to the where the ligand is docked. So whatever atoms
which is within maybe say 3 angstrom of my ligand, i take those atoms and
get the average as the center of my grid. I don't know about your receptor
or ligand but I hope this maybe will help.

Regards,
Rowyna

_____________________________________________________

Hi Johanna, can you just change the grid parameter file so that the 3D
cube only encompasses the active site? Then you will only be able to
search within this area.

Simon Cross
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Define the x,y,z coordinates of the center of your active site, then in
your glg file change the x,y,z coordinates of the grid center with your
data. In addition to this you can specify the dimensions of your grid box
based on the active site of the protein.

Istvan