Subject: autodock3 and flexable ligand

From: Tzvika Aviv <[email-masked]>
Date: Thu, 02 Dec 1999 18:55:18 +0200

Hi all

I'm trying to dock a peptide to an enzyme, since I know the binding site
I want to use autodock3 to search for the best conformotion of the
ligand in it's place (not using the random initation). I tried to use
this parametrs at the .dpf file:

# Initial Translation, Quaternion and Torsions
tran0 0.0 0.0 0.0  # initial coordinates/A or "random"
quat0 1.0 0.0 0.0 0.0  # initial quaternion or "random"
ndihe 30  # number of initial torsions
dihe0 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.

but the peptide moves out of the binding site. (when I use the peptide
as a rigid molecule, It is not moving out).

Does anybody know how to set the parametrs for this kind of runs? (a
conformation search on a ligand at a binding site)

tzvika

tzvika aviv
e-mail: [email-masked]
pharmacy school
hebrew university
jerusalem