ADL: regarding active site

kaustubh kaustubh.joshi at
Mon Jun 22 02:31:43 PDT 2009

I tried running autogrid4 using the gpf file u forwarded. But it showed some
related to atoms defined in receptor.
Sorry do not have exact error with me just now to paste here. Will do so one
my system is free to run it again.

BTW, suggestion by Sargis worked. Seems there was some bug which created
If I give gridcenter as -3.227 -33.066 21.673, then the problem of grid
genration at the remote place used to appeat, 
but as Sargis suggested if I modify it to -3 -33 21 then it works well. Now
I am able to generate the interactions at the expected sites. He said this
bug has been taken care of the new version of autodock. I need to look into
Could you please let me know the new version number of autodock where it

I am yet to look into the query you asked me to check in glg file. Will
respond soon on that. 
Anyways, thanks to you all specifically Bagdevi for taking effort in
resolving the problem, Ruth and no to forget Sargis whose suggestions help
the most.


bagdevi wrote:
> kaustubh,
> I tried generating map files used the gpf you had attached with the
> mail.  And it did not work. Thus I generated a new gpf using the
> 3DM2.pdbqt and lig.pdbqt you had send. The resulted gpf I used to make
> map files and it further run autodock4.
> And all worked well, the lig.pdbqt got docked inside the grid where
> the original ligand of the complex lied.
> I am attaching this gpf. You run autogrid4 using this.
> Make dpf using the ligand and receptor you had send. And see the results.
> If it worked well, we can understand there is some error, while you
> are making the gpf file.
> Regards,
> Bagdevi Mishra.
> On Wed, Jun 17, 2009 at 12:52 PM, Oleg Trott <trott at> wrote:
>> On Tue, Jun 16, 2009 at 10:22 PM, Davide
>> Mercadante<dmer018 at> wrote:
>> > can I just go through
>> > the installation of autodock-vina without removing autodock4?
>> Yes
>> --
>> Oleg Trott, Ph.D. (Columbia University)
>> ________________________________________________
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> ________________________________________________
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