The Molecular Graphics Laboratory Forum

AutoDock, AutoLigand, MGLTools, Vina, PyRx and more.
It is currently Tue May 23, 2017 3:04 am

All times are UTC




Post new topic Reply to topic  [ 2 posts ] 
Author Message
 Post subject: Help Vina
PostPosted: Mon Nov 30, 2015 12:40 pm 
Offline
Millimolar User
Millimolar User
User avatar

Joined: Mon Nov 30, 2015 8:12 am
Posts: 2
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/


Top
 Profile  
 
 Post subject: Re: Help Vina
PostPosted: Tue Feb 07, 2017 12:54 pm 
Offline
Millimolar User
Millimolar User
User avatar

Joined: Tue Oct 07, 2014 6:34 pm
Posts: 2
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


Top
 Profile  
 
Display posts from previous:  Sort by  
Post new topic Reply to topic  [ 2 posts ] 

All times are UTC


Who is online

Users browsing this forum: No registered users and 1 guest


You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot post attachments in this forum

Search for:
Jump to:  
cron
POWERED_BY
Translated by Maël Soucaze © 2009 phpBB.fr