Subject: Autodock bad energies and positions

From: "Teran Castañon, Hugo Gutierrez de"<[email-masked]>
Date: Tue, 25 Jun 2002 10:29:17 +0200

For the Autodock users community: 
I have obtained bad results from a docking experiment with Autodock
default parameters (CONH atom types, 12-6 lj for N), in order of
energies (-30000 kcal/mol, unreallistically good) and position (legand
clearly shows bumps with the protein). on the mayority of solutions
found. 
Does anyone have expirience on such Autodock results? 
If I change parameters (12-10 hb for N, and creating a new atom type
12-6 lj for nitrogen that does not accept H-bonds, and considering only
polar H on my ligand) solutions are more reallistic, but don't agree
with experimental data. 
Anyone have expirience on changing Autodock default parameters or
creating new atom types? 
Thanks in advance, 
Hugo 
-- 

Hugo G. de Teran Castañon

Drug Design laboratory

Research Group on Biomedical Informatics (GRIB) - IMIM/UPF

C/ Dr. Aiguader, 80                     Tel: +34 93 221 1009

E-08003 Barcelona (Spain)               Fax: +34 93 221 3237

e-mail: [email-masked]          http://www.imim.es/grib/
<http://www.imim.es/grib/>