Hi Adil,

Vina has other options that control the number of outputs:

--num_modes -> is the number of complexes that vina will return, the default value is 9 and the maximum number returned is 20, so if you want to get 100 complexes you have to run vina 5 times with - num_modes 20.

--energy_range -> After looking at the photos you attached, I'm pretty sure that's the problem. The default option here is 3 kcal/mol, which means that vina will return results if the last complex is less than 3 kcal/mol different from the first complex. Your first result has -8.7 kcal/mol and the last one -6.3 kcal/mol gives a difference of -2.4 kcal/mol, which means that the other result has more than 3 kcal/mol, that's why you only get 2-3 results. For more results, you should use a value greater than 3.

From my experience, the problem of time can be due to two reasons in particular:

1-The ligand and the receptor are too large (they have many atoms),

2-you are using too many rotatable bonds on both the receptor and the ligand (I saw that you use the fixed receptor but maybe the ligand has too many rotating links), and

3-cpu usage is low, vina allows you to specify the number of cpu to use (--cpu), the default is 1, if you have the possibility to increase the number, you can speed up the calculation

I hope my comments are useful

Sincerely

Daniel

Daniel Alpízar Thank you for the explanation. How can we change the value to greater than 3? Also, I read somewhere that if we can edit the following par.mc.num_saved_mins = 20;

to

par.mc.num_saved_mins = num_modes; in main.cpp source file, it will give 100 confirmations. But I think it works for Linux. Do you think it can work for windows also?

Sneha Kandapal To change the energy range you just have to include in your vina command in the console the variable - energy_range #, where # is the cut you want to use.

The last question I'm not really sure, but it should work on both, my advice is to save the original source file main.cpp, make the change and try, if it works you can keep the change, if not replace the file with the one you saved before.

I hope it help you

Best regards

Daniel

Sneha Kandapal download vina_1.2.3 (https://autodock-vina.readthedocs.io/en/latest/), it already has implemented the change to obtain more than 20 results and some other upgrades. You can read more here

J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli. (2021). AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings. Journal of Chemical Information and Modeling.

Best Regards