ADL: High RMSDs

ANURAG BAGARIA anurag.bagaria at gmail.com
Mon Jan 21 00:08:09 PST 2008


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


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