davitikharchilava / autodock_vina_runner Goto Github PK

#AutoDock Vina docker

Requirements:

• python3
• pip3
• 'texttable' package

####Autodock Vina multi-ligand docking!

In the command line you need to type the name of a protein correctly (after the 'python3 vina_runner.py ') to let the script start the docking with Autodock Vina.

Command line command example ==> python vina_runner.py -c conf_6m71.txt -o C:/Program1/TSRI/vina/test/ (-o and path can be optional).

The written protein name represents the conf_PROTEIN.txt config file which must be located in the same directory as 'vina_runner.py'. Config file must be set up properly for docking too.

####USER MANUAL:

USER MANUAL FOR SETTING UP conf_[PROTEIN].txt CONFIGURATION FILE:

ligpath => Directory of a ligands which are going to be docked to a protein

receptor => File name of a protein macromolecule (PROTEIN.pdbqt)

freceptor => Full directory path for protein file

vina_dir = C:/Program1/TSRI/vina/vina.exe => Autodock Vina installed directory

output_dir => Docking output directory by default (can be changed manually from command line)

Autodock Vina docking grid box parameters and system usage:

strcenter_x

strcenter_y

strcenter_z

strsize_x

strsize_y

strsize_z

strcpu => Number of CPUs used for docking process (by default it's 8)

strexhaustiveness => Level of being more accurate (by default it's 8)

strnum_modes => Number of Autodock Vina runs (by default it's 9)

\

• Both ligands and proteins must be prepared for docking and converted in .pdbqt format.
• For each protein docking new conf_PROTEIN.txt configuration file must be created.
• There must not be deleted or modified any variables' names above.
• After each "=" 1 blank space must be made(" "), as it is done for "vina_dir = C:/Program1/TSRI/Vina/vina.exe".
• for the receptor there needs to be written receptor file name (NAME.pdbqt).
• All the directories can be written with single "/".
• After configuring this config file, it must be named after a protein name (conf_PROTEIN.txt) for which this config is created. It must be located in the same directory as "vina_docker.py".
• If the docking is re-running with same ligand and protein, but there is changed only grid box parameters, be aware that in the output directory older version of output file will be replaced with the newer one, or change the next output directory to avoid such result.
• script will use output_dir line as a default docking output directory, from the command line this directory can be changed manually. Either way if the output_dir does not exist there will be created one.
• output_dir path must be written with ending '/' (ex: C:/Program1/TSRI/vina/test/ <= last '/' must be presented!)
• command line command example: python vina_runner.py -c 6m71 -o C:/Program1/TSRI/vina/test/ (-o and path can be optional)

Have a happy docking!