ADL: Very High RMSD as compared to the experimental complex conformations

ANURAG BAGARIA anurag.bagaria at
Tue Jan 15 23:50:54 PST 2008

Dear Members / users of Autodock,

I was just wondering if someone could help me out with this problem.

I am trying to validate and reproduce the results of some of the
experimentally known protein-ligand complexes by keeping the original
receptor as such (original co-ordinates retained) and translating the ligand
and then docking it back using Autodock3, but I have constantly been getting
very High RMSD between the original and docked ligand conformations (ranging
from 2 Angstroms to 12 Angstroms). I have been trying out playing with
different parameters in the docking parameter file as well as the grid
parameter file but have not been able to obatin conformations with reduced
RMSD even after running over 100 runs of the genetic algorithm.

I would be grateful if someone could tell something about the search space
of ligand in Autodock3, that is how much space (what radius) is the ligand
allowed to move once the gridcenter is defined in the grid parameter file.
This could sort out my problem as I could restrict the ligand's movement
into a particular volume (space) about the specified grid-center.

Looking forward to a positive response from the members.

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


More information about the autodock mailing list