ADL: autodock Digest, Vol 62, Issue 15

Jacya Aiman jacyapk at gmail.com
Sat Oct 31 22:52:24 PDT 2009


Dear all
Can anybody please clarify how to view interactions between the ligand and
the protein after docking.
Jacya
On Sun, Nov 1, 2009 at 12:30 AM, <autodock-request at scripps.edu> wrote:

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> Today's Topics:
>
>   1. Re:  Is there a minimum size for the grid box??
>      (Davide Mercadante)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 31 Oct 2009 10:43:38 +1100
> From: Davide Mercadante <dmer018 at aucklanduni.ac.nz>
> Subject: Re: ADL: Is there a minimum size for the grid box??
> To: autodock at scripps.edu
> Message-ID:
>        <1da69e140910301643o23d8638bgac4166aa3fc7de75 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hello,
>
> did you check the position of the ligand after your calculation? Is it in
> the box?
>
> If is not in the box but is far from the protein it is due to a bug in the
> software. In this case you need to change in the glg file the coordinates
> of
> the box changing it in all integers...
>
> example:
>
> If you have the box coordinates as the following floats: 49.521 2.365
> -5.012
>
> change them in: 49 2 -5
>
> Then run autogrid and then autodock.
>
> Cheers,
> Davide
>
> 2009/10/31 Nicolas SAPAY <nicolas.sapay at cermav.cnrs.fr>
>
> >
> > >
> > > Hi all,
> >
> > Hello Jerome
> >
> > >
> > > recently I prepared several Autodock calculations (4.2) with a series
> of
> > > ligands and 2 different proteins. After a while I saw that final
> binding
> > > energies were in the range of +100,000 kcal/mol for all of them!!
> > >
> > > Then I changed the grid box dimensions from 36;38;40 to 36;60;40 and it
> > > worked fine, I got binding energies around -20 kcal/mol... And you know
> > > what? If I use 36;58;40 energies are back in the +100,000 kcal/mol
> > > range...
> > > wierd, or do I do something wrong?
> >
> > This probably means that your ligand is outside the grid. There is a
> > strong energy penalty in such case. Your grid should be big enough to
> > allow the ligand to rotate. 38 points along the y axis represent ~14.5 A
> > (assuming a grid spacing of 0.375 A). 60 points represent ~22.5 A. Is
> that
> > big enough for your ligand?
> >
> > Another explanation could be that the (potential) binding site of your
> > ligand is not entirely covered by the grid with 38 points, but is with
> 60.
> > You can check the positions of the grids and of the best docking model
> > with ADT.
> >
> >
> > Have a nice week end,
> > Nicolas
> >
> > >
> > > This was with the first protein... but I experienced the same issue
> with
> > > the
> > > other one, instead of 40;40;42 I had to use 46;56;42 as minimum box
> size
> > > in
> > > order to get correct binding energies.
> > >
> > > Does anybody already experienced such issue, or does anybody know where
> > it
> > > could come from?
> > >
> > > Thanks for your help.
> > >
> > > -----
> > > Jerome
> > >
> > >
> >
> ????????????????????????????????????????????????????????????????????????????????????????
> > > Jerome Baffreau, PhD
> > > Universite de Montreal
> > > Montreal, QC - CANADA
> > >
> > > --
> > > View this message in context:
> > >
> >
> http://n2.nabble.com/Is-there-a-minimum-size-for-the-grid-box-tp3918971p3918971.html
> > > Sent from the AutoDock mailing list archive at Nabble.com.
> > >
> > > ________________________________________________
> > > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list---
> > >
> > >
> >
> >
> > --
> > [ Nicolas Sapay - Post-Doctoral Fellow ]
> > CERMAV - www.cermav.cnrs.fr
> > BP53, 38041 Grenoble cedex 9, France
> > Phone: +33 (0)4 76 03 76 44/53
> >
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
>
>
>
> --
> Davide Mercadante - PhD student -
> Department of Chemistry
> The University of Auckland
> Rm 438 ext. 89171
> 1142 Auckland, New Zealand
>
>
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> End of autodock Digest, Vol 62, Issue 15
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