ADL: regarding active site

kaustubh kaustubh.joshi at systemsbiology.fi
Fri Jun 12 05:32:09 PDT 2009




@Davide

How did you "Manually" positioned the ligand in the active site? Using
AutoDock?
If so please share!!


Davide Mercadante wrote:
> 
> Dear Andreas,
> 
> actually this happened also to me. I "manually" positioned my ligand in
> the
> known active site of the enzyme and I centered the box on one atom of one
> of
> the residues that compose the active triad of my enzyme.
> 
> However, after the calculations, I went to visualize the conformations
> generated but the ligand just disappeared from the active site going
> somewhere else.
> Please, can you help me to understand why that happened and how can I
> solve
> the problem?
> 
> Thanks infintely in advance for your help.
> 
> Best Wishes,
> Davide
> 
> Davide Mercadante - PhD student -
> Department of Chemistry
> Faculty of Science
> The University of Auckland
> Auckland 1142, New Zealand
> 
> 2009/6/12 Kukol, Andreas <a.kukol at herts.ac.uk>
> 
>> 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 scripps.edu
>> [mailto:autodock-bounces at scripps.edu]
>> On
>> > Behalf Of kaustubh
>> > Sent: 12 June 2009 11:09
>> > To: autodock at scripps.edu
>> > 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?
>> > --
>> > View this message in context:
>> http://n2.nabble.com/regarding-active-site-
>> > tp3066853p3066853.html
>> > Sent from the AutoDock mailing list archive at Nabble.com.
>> >
>> > ________________________________________________
>> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
>> ---
>>
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>>
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> 
> 

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