Hi, I'm trying to dock thousands of compounds using autodock vina. I already have the script for running the compounds without manually docking them one by one on the GUI of autodock tools.
However, I have thousands of ligands that I need to prepare and this is very time-consuming. Can someone help me with how I can prepare all the ligands all at once in a single batch? What I am currently doing is using the autodock tools GUI, then clicking Ligand > open > file > save as pdbqt. With the Ligand option in autodock tools, it sets the gasteiger charges, merges the nonpolar hy drogens and sets the TORSDOF. Is there a script which I can use so that I can perform the same without the need to manually use the GUI for each compound? thank you!
Hello,
You can use prepare_ligand4.py package of AutodockTools to prepare pdbqt of ligand. The package can be found at MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24.
And you can also use open babel
http://openbabel.org/wiki/Category:Capabilities
Then you would easily perform a large number of docking.
It is also useful to read this article
https://doi.org/10.1021/acs.jcim.1c00203
hello Rezvan Marjani thank you for your response. Do you have a tutorial for the MGL tools prepare_ligand4.py? thanks!
1.Preparing Ligands
At first, locate the ‘prepare_ligand.py’ (or ‘prepare_ligand4.py’ for Autodock4) file in the MGLTools directory you have already installed. The script will be present in /path/to/mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs
or download from https://github.com/MunibaFaiza/Virtual-Screening_files/blob/main/prepare_ligand.py
Or
https://bitbucket.org/Bioinformatics-Review/virtual-screening-files/src/master/prepare_ligand.py
Keep your ligands in a directory in pdb format and run this script as follows:
$ python prepare_ligand.py -l ligand.pdb -v -o ligand.pdbqt
Here, -l defines the ligand filename, -o is the output file, and -v is for displaying processing (default is minimal output).
There are other arguments that you can define such as
-d dictionary to write types list and number of active torsions “
-A type(s) of repairs to make:\n\t\t bonds_hydrogens, bonds, hydrogens (default is to do no repairs)”
-B type(s) of bonds to allow to rotate.
-M interactive (default is automatic output), and so on.
To know more options, type $ python prepare_ligand.py -h.
You can set parameters for the first ligand PDB file and then use the same command for all ligand files.
2. Prepare receptors
Similarly, receptors can be prepared from a Python script ‘prepare_receptor.py’ (or ‘prepare_receptor4.py’ for Autodock4) present in the directory mentioned above. You can also download it from
https://github.com/MunibaFaiza/Virtual-Screening_files/blob/main/prepare_receptor.py
Or
https://bitbucket.org/Bioinformatics-Review/virtual-screening-files/src/master/prepare_receptor.py
Keep your receptor files in a directory in pdb format and run this script as follows:
$ python prepare_receptor.py -r receptor.pdb -v -o receptor.pdbqt -A
Here, -r defines the receptor filename, -o is the output file, -v is for displaying processing (default is minimal output), and -A is used for checking hydrogens.
For more arguments, type $ python prepare_receptor.py -h.
Good luck🌾
Rezvan Marjani thank you for your response! i'm using windows though
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