See these links:

Article AMDock: a versatile graphical tool for assisting molecular d...

https://www.researchgate.net/topic/AutoDock-Vina

https://www.researchgate.net/topic/AutoDock-4

http://autodock.scripps.edu/faqs-help/tutorial/using-autodock-4-with-autodocktools/2012_ADTtut.pdf

Article AutoDock4(Zn): An Improved Auto Dock Force Field for Small-M...

see this link

https://pubs.acs.org/doi/10.1021/ci500209e

Dear Remal Al-Gounmeein

Thank you very much for the answer and the links sent, but I didn't find the solution to my problem in them.

Also, it is not interesting for me to use AMDock because my intention is to run autodock4 and vina from python.

I found a script for Vina in which it is possible to use the ad4 scoring function.

https://autodock-vina.readthedocs.io/en/latest/docking_python.html

Since what I want to do is to run vina and autodock4 from python. If using the ad4 function in this script is the same as doing the whole autodock4 process, it will make my job much easier.

On this same site under "Frequently Asked Questions", there is an answer, "AutoDock Vina inherits some of the ideas and approaches of AutoDock 4", (...) "However, the source code, the scoring function and the actual algorithms used are brand new, so it’s more correct to think of AutoDock Vina as a new “generation” rather than “version” of AutoDock."

I want to evaluate the performance, i.e. which of the two programs is better for my study. It is not clear to me if using this script just change the scoring functions is the same as using each in their respective processes separately.

Dear Dler Kadir ,

Thanks for the help.

But I don't have zinc in my simulations.

My doubt is only about the differences between autodock4 and vina.

I would like to know if I just change the scoring function in this script is the same as doing the whole procedure for autodock4

https://autodock-vina.readthedocs.io/en/latest/docking_python.html