ADL: Autodock: High RMSD between Experimental and Docked ligand conformations

ANURAG BAGARIA anurag.bagaria at
Thu Jan 17 01:49:16 PST 2008

Dear Rob and Members of Autodock list,

First and foremost, thanking Rob for his valuable suggestions on my query
regarding obtaining high RMSD between the docked ligand conformation and the
experimental complex ligand conformation.

I would also like to bring into notice a few points with reference to Rob's
suggestions so that my Problem becomes more clear:

1. In my case I had "cleaned up"  and curated the original receptor-ligand

2. The RMSD range of 2 Angstroms should not have been a problem, had that
been for the ligand with minimum docked energy. But those positioned as
cluster Rank 1 (based on docked energy) by AUTODOCK3 have far higher RMSDs
(even upto 12 Angstroms). A number of times those ligands having very high
docked energy show up lesser RMSDs and even visualising them in viewers
shows conformation closer to Experimental conformations.

3. Observing the RMSD Table in the docking log file, I find that the
Reference RMSD has even greater variation range (starting from 12 Angstroms
to 23 Angstroms).

I would be grateful if someone could explain me these High values for
Reference RMSDs or a method so as to bring them down so that I could
optimize between low RMSD and low Docked Energy. (This value for a
receptor-ligand complex system obtained from the internet is 0.7 to
1.5Angstrom ... quite low indeed as compared to Reference RMSD values
in the
case my experiment with a different complex).

Looking forward to a positive response.

The road to success is always under construction ...!!!


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