Subject: AutoDock torsional restraints

From: Margaret Johnson <[email-masked]>
Date: Mon, 18 Mar 2002 16:00:21 -0800 (PST)

Just wondering if someone could suggest to me how to properly restrain
torsion angles in AutoDock. I am trying to dock flexible ligands to a
protein, using LGA, while applying restraints to allow only a small amount
of flexibility in the torsion angles. When I use the command "hardtorcon",
the program doesn't seem to apply a barrier at all. With "gausstorcon" and
a barrier of 100 or more, there is a little flexibility but not enough.
When I lowered the barrier to 10, it seemed to work at first, but later on
I noticed a lot of conformations produced with torsional angles far
outside the range. What are the units of this barrier and how/when is it
applied in the calculation? Is this energy added to the internal energy of
the ligand, or does it not appear in the final docked energies at all? And
how can I get the program to show this penalty ("showtorpen" doesn't seem
to work?)

Any suggestions would be much appreciated. Thanks and best regards,

Maggie Johnson

Margaret A. Johnson
Department of Chemistry
Simon Fraser University
Burnaby, B.C.
Canada
Tel: (604) 291-5650
Email: [email-masked]