AutoDock Vina Pose Reproduction Tutorial

This tutorial is to teach the user how to dock molecules using AutoDock Vina. This tutorial will utilize many of the same scripts and parameters

(Important Note: If you already conducted an AutoDock4 experiment previously, you can work in that directory and skip to Part IV,the Docking step)

II.Prepping Directories

First step is prepare a file with a list of systems within it. For this docking experiment this file was called clean.systems.all

121P
181L
182L
183L 
184L
etc

Second step run the run.000.AutoDock.source.sh script to prepare a directory for each system in the file.

The 1st arguement is the list of systems file made in the previous step.

The 2nd Arguement is the new directory that will be made where all the AutoDock Vina experiments will be performed

bash ./run.000.AutoDock.source.sh ../clean.systems.all AutoDock_Vina_Tutorial

The directory where all the directories will be formed is

AutoDock_Vina_Tutorial/

Each System will have it's own directory in this file

AutoDock_Vina_Tutorial/121P/
AutoDock_Vina_Tutorial/181L/
AutoDock_Vina_Tutorial/182L/
etc

III.Preparing Receptors and Ligands

For this part of the experiment, the receptors and ligands were prepared into pdbqt format. To accomplish this part of the experiment the original mol2 files were used from the testset to convert these systems. The ligands will be assigned gasteiger charges and am1bcc charges will be assigned to the receptor, which produced the highest success rates in previous experiments and was performed in previous papers. Scripts were developed to process these systems from mol2 to pdbqt. The charges of these systems aren't a key factor because AutoDock Vina doesn't rely utilize th

Command to convert these files

Step 1) Make sure you are in the correct directory

cd AutoDock4_Tutorial/

Step 2) Run the correct bash script to run these molecules

bash ./../run001.AutoDock4.system.prep.sh /gpfs/projects/rizzo/yuchzhou/RCR/DOCK_testset/clean.systems.all ../AutoDock4_Tutorial

This script will create a ligand and pdbqt receptor in each system directory

cd 121P/
ls

121P/121P.lig.am1bcc.pdbqt
121P/121P.rec.clean.pdbqt

Further Processing may be needed to prepare these systems, will explain later

This scripts used to accomplish this were prepare_ligand4.py and prepare_receptor4.py found in mgltools/1.5.6

IV.AutoDock Vina Docking

(Note: You can start here if you finished the AutoDock4 Tutorial already) This part of the project will deal with the docking the molecule properly using a script, that generates a gpf using mgltools, creates the input parameters for docking, then performs all the AutoDock Vina Experiments

The grid parameter file, gpf is generated to determine the center of the ligand which is where the binding site is located, an essential step for this process to work.

Following this, a parameter will file will be generated for each system containing the ligand, receptor, the grid center, and the grid size.

Default grid sizes

receptor=1AGW.rec.clean.pdbqt
ligand=1AGW.lig.am1bcc.pdbqt

center_x=10.354
center_y=3.962
center_z=21.128

size_x=15
size_y=15
size_z=155

out=1AGW_vina.pdbqt

This generates a list a list of 10 different pdbqt files to study

The script will implement a command to split all the AutoDock Vina pdbqt results into multiple pdbqt files