ADL: Docking inside recptor / Screening using Cygwin on a PC

David Crosby dcrosby at
Tue Mar 11 13:21:59 PDT 2008

Hello everyone, first I'd like to thank the developers of Autodock and ADT
for making such fabulous software freely available, it's a great model I
hope other developers follow!


I have two questions; the first is likely more simple to answer than the


1)       I've noticed often when I attempt to dock a ligand I'll get a
handful (perhaps 5 in 25-50) of dockings where the ligand is docked quite
literally inside the macromolecule resulting in some astronomical dG value.
Is there some setting I'm missing when I set up my grids or docking
parameters to tell Autodock to avoid nonsensical dockings?  I see you can
specify an upper energy limit under the docking parameters menu, but can I
assign a lower limit to avoid these wild results?  They throw off the
clustering data.  I'm attempting to dock a somewhat small molecule with 4-6
torsions onto a relatively small receptor (~6kd,)  I'm trying to keep my
initial dockings unbiased, so my grid envelops the entire receptor. I've
left plenty of space for the ligand to rotate freely in all configurations,
so why does my ligand often end up inside my receptor instead of on the
surface?  I understand autodock first introduce 50 randomly placed/oriented
ligands inside the grid volume and make calculations from there, but why
would it consider molecules making obviously high-energy (or low) contacts
with other atoms as preferable dockings?


2)       I'm curious if anyone out there is screening virtual libraries
using Windows XP and the Cygwin linux-like environment?  The tutorial at the
Autodock homepage has great instructions in a UNIX native environment, but
I'm hoping someone out there may have some helpful tips on translating that
protocol into the Cygwin environment.  I'm primarily interested in screening
the NCI's diversity set.


Thanks in advance!


David Crosby


Experimental Pathology

Med Surge II, Rm 311

University of California, Irvine, CA 92617

email:  <mailto:dcrosby at> dcrosby at


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