I am able to screen single ligands using Autodock in Cygwin. However, I want to screen large number of ligands to get a good inhibitor. Can you please let me know about link to any manual or tutorial that covers screening of multiple ligands.
Thank You Danish
I tried it. It looks really Cool.
Thanks a lot
Murli
i will suggest you to install linux in system which will help you in docking of multiple ligands at the same time(around 8 ligands at a time,depending on system configuration).
You can use PyRx interface (https://pyrx.sourceforge.io/), which gives the option to use autodock 4 as well as vina to screen a library of ligands. Alternatively, you can follow the instruction given in the Vina website (http://vina.scripps.edu/manual.html#screening) to run a batch job. The same script can be tweaked to run batch job with AutoDock 4 as well.
You can use the config file to virturally screen ligands against a single receptor using Vina version 1.2.3 which now allows for batch mode. The updates to this version (July 2021) are covered in the following article: doi.org/10.1021/acs.jcim.1c00203. The newer version gives you a choice of forcefields as well as other expanded docking methods (i.e. Simultaneous Multiple Ligand Docking, Hydrated Docking, a specialized force field to model zinc-coordinating ligands, and Macrocycle Conformational Sampling).
- The source code is available at https://github.com/ccsb-scripps/AutoDock-Vina.
- Install and tutorials for Autodock Vina 1.2.3 are available at: https://autodock-vina.readthedocs.io/en/latest/introduction.html
Here are the contents of the conf_batch.txt file that you will call from using "vina --config conf_batch.txt" when in windows or "vina --conf conf_batch.txt" when in macOS or Linux.
receptor= receptor.pdbqt
batch= ligand1.pdbqt
batch= ligand2.pdbqt
dir= results
center_x= 9
center_y= -3.5
center_z= -15
size_x= 50
size_y= 52
size_z= 62
exhaustiveness= 64
num_modes=50
**Note: When in batch mode, you will need to specify "dir=folder". This is the folder that vina will write your results in. You should create this folder in the same location as your conf_batch.txt folder. I have called this folder "results".
This is a much easier way to run multiple ligand screens than to use a script that is specific to your OS.
Justin D Fair sir, is it possible to use batch mode for multiple ligand simultaneous docking? For example, I want to keep ligand 1 common and ligand 2 to change after each docking. Is there any way I can perform this using Vina 1.2.3? Any guidance in this regard will be very helpful. Thank you.
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