ADL: regarding active site

Davide Mercadante dmer018 at aucklanduni.ac.nz
Fri Jun 12 05:09:34 PDT 2009


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.
> >
> > ________________________________________________
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>
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