Preparation for Autodock GPU Docking

[NexabioSolutions]

Hello, I am currently trying to utilize the Autodock GPU repo. to dock ligand and proteins. In regards to the usage of this, what exactly is the process required to be able to prepare both ligands and proteins for docking? based on the example files and the inputs what seems to be the case is that there must be an inclusion of several files as shown in the screenshot. My question is if I would like to use the autodock GPU how can I configure the following:

1. Being able to generate all the required files and proper formats of files for docking for the protein, setting up the grid box and downloading all the required files to be able to run the analysis
2. Being able to generate all required files for ligand and getting them in proper format.
3. I would like to be able to create a systematic pipeline that will take in SMILES strings, change them into the proper pdbqt format (this can be done on our end) and from Amino Acid Sequence use alpha fold to get pdb and then convert to pdbqt using openbabel. What other steps or packages would be required to prepare the rest?
4. What is the command to initiate the run and what are the exact files and formats needed to be able to get the binding energies, and how can I also view the several poses? Is this contained in the DLG File? Is there a way to parse the DLG File?

These would be a tremendous help - - thank you.

[diogomart]

Hello, see here: https://meeko.readthedocs.io/ specially the basic docking tutorial