ADL: regarding active site

Kukol, Andreas a.kukol at herts.ac.uk
Fri Jun 12 06:59:16 PDT 2009


You need to save the ligand after moving, with the transformed coordinates.

It is possible that the ligand moved out of the binding site after docking, in  that case AutoDock has found a more favorable position. It should, however, not move outside the gridbox.

Andreas
> -----Original Message-----
> From: autodock-bounces at scripps.edu [mailto:autodock-bounces at scripps.edu] On
> Behalf Of Davide Mercadante
> Sent: 12 June 2009 13:39
> To: autodock at scripps.edu
> Subject: Re: ADL: regarding active site
>
> Hi,
>
> I just did it using pmv given with autodock tools. However, the problem
> remains because after the calculations my ligand was not there anymore.
>
> how to position the ligand is explained here. Here is also written that you
> can only move the ligand inside a grid. This means that I have to move the
> ligand in the active site just after I create the grid box?
>
> http://autodock.scripps.edu/faqs-help/how-to/positioning-the-ligand
>
> How I can solve the problem?
>
> Thanks,
> Davide
>
> 2009/6/13 kaustubh <kaustubh.joshi at systemsbiology.fi>
>
> >
> >
> >
> > @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
> > >> ---
> > >>
> > >> ________________________________________________
> > >> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list---
> > >>
> > > ________________________________________________
> > > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> > >
> > >
> >
> > --
> > View this message in context:
> > http://n2.nabble.com/regarding-active-site-tp3066853p3067408.html
> > Sent from the AutoDock mailing list archive at Nabble.com.
> >
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
> ________________________________________________
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