ADL: High RMSDs

Kalidas Y kalidas.y at gmail.com
Mon Jan 21 20:42:01 PST 2008


Dear Anurag

 Please check if the ligand is there in the same binding site or elsewhere
on the surface of the protein w.r.t actual (crystal) ligand
(1) You may do an initial positioning of the docking grid by setting
'' gridcenter '' in the .gpf file to the centroid of the coordinates of
ligand atoms.
(2) You can restrict the size of the grid to encompass only the site of
interest.

With Regards
Kalidas. Y



On Jan 21, 2008 1:38 PM, ANURAG BAGARIA <anurag.bagaria at gmail.com> wrote:

> Dear Members and visitors of Autodock Mailing list,
>
> I have been trying to reproduce the docked conformation of a few
> experimental complexes by docking the translated and transformed ligand
> back
> into the original receptor (file). The docked ligand conformations
> generated
> after docking give a very high range of RMSD from the experimental ligand
> conformation (2 Angstroms to 15 Angstroms) for the same receptor-ligand
> complex.
> Moreover, the ligand with docked Energy Rank 1, most of the times, is the
> one with comparatively higher RMSD (The higher ranks seem to give closer
> structures with lower RMSDs).
>
> I would be grateful if someone could suggest me some parameters (in the
> docking parameter file or/and grid parameter file) so as to get better
> correlated results.
>
> Looking forward to a positive response.
> Regards.
> --
> The road to success is always under construction ...!!!
>
>
> ANURAG KUMAR BAGARIA
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>



-- 
Thanking You
With Regards
Kalidas Y

http://ssl.serc.iisc.ernet.in/~kalidas

"Love will warn you against advising another to do something that you,
yourself, do not want to do - Baba"

"You May Not Always Oblige, You Can Speak Obligingly." - Baba


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