ADL: regarding active site

Bagdevi bagdevi.mishra at gmail.com
Tue Jun 16 03:54:22 PDT 2009


I checked the dlg file you had send and the picture you have attached as
well.
I guess you are running your autogrid4 from adt, is not it?

Do try to run autogrid4 from command line using the following command
See, if you get grids around the place where you want it to be.

autogrid4 –p <receptor>.gpf –l <receptor>.glg


Regards,
Bagdevi Mishra.



On Tue, Jun 16, 2009 at 1:54 PM, kaustubh
<kaustubh.joshi at systemsbiology.fi>wrote:

>
>
> The problem is not about not being able to select the atoms. Its about the
> generation of grid at appropriate and expected position.
> Am attaching a scrrenshot, where you can see my protein structure with
> selected residues around the native ligand on right hand side below.
> On the upper surface you can see the docked structure in molecular surface
> form with a cubical grid around it.
> The issue is, I asked autogrid4 to generate this grid around the native
> ligand but every time it generates this grid on shown site and not the
> expected site/
> Since the molecule will dock at position where the grid is generated, I
> guess the problem is associated with grid generation and I am not able to
> solve this.
>
>
> http://n2.nabble.com/file/n3085076/Screenshot.png Screenshot.png
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