The Molecular Graphics Laboratory Forum

Hello,

I have several questions about AutoDock Vina:

Can I perform a blind docking between a DNA/protein complex and a ligand?
What really represents the exhaustiveness parameter (number of independent runs, .....?)
Why the number of binding modes seems to be limited to 20?
How many runs are performed in a docking experiment?

The config file that I test is the following, does it seem correct to you?
Thank you very much for your advices.

Norbert

receptor = receptor.pdbqt
ligand = ligand.pdbqt

center_x = 45.4
center_y = 53.0
center_z = 43.7

size_x = 69.7
size_y = 69.7
size_z = 69.7

cpu = 12
out = conf.pdbqt
log = conf.log



num_modes = 50
energy_range = 100
exhaustiveness = 10000

--
Dr. Norbert GARNIER
Assistant Professor of physics - Orléans University

« DNA repair: structural and functional approaches»
Centre de Biophysique Moléculaire, UPR4301, CNRS
Rue Charles Sadron
CS 80054
45071 Orléans cedex 2
Tel: +33 (0)2 38 25 76 68
Web site : http://cbm.cnrs-orleans.fr/

Hi Norbert,

Should this still interest you, I deal with exhaustiveness etc at great length in the paper mentioned in below post, make sure to look at the supplementary file #2, section "docking" too.

viewtopic.php?f=12&t=2949&e=0

Best,
Rob

thank you