ADL: regarding active site

kaustubh kaustubh.joshi at systemsbiology.fi
Tue Jun 16 04:35:19 PDT 2009


No I haven't used ADT to generate grid. I did it using command line only. 
Just for gpf file creation I used ADT, that too because I was attempting it
concentrating on specific points in the protein.
( I do have generated gpf files from command line in earlier attempts but
that did not changed the results).
Even I realized that results obtained from command line calculations are
more worth than from ADT. SO that is not an issue.

Kaustubh


bagdevi wrote:
> 
> 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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