Use AutoDock Vina (smina)

The PDB file containing the receptor protein structure to predict protein-ligand complexes with.

The chemical structure of the ligand you want to bind. For PDB files ensure that your protein/peptide is 40 residues or less and only contains a single chain / molecule. For SMILES inputs ensure that Local Only is not checked as the position SMILES defined molecules are ambiguous.

Specify the builtin scoring function you want to use.

The docking algorithm will focus on exploring the immediate vicinity of the ligand's initial position, rather than performing a global search across the entire receptor surface. This approach can be useful when you have a good idea of the ligand's binding site and want to refine the docking within that specific region. However, this might miss potential binding sites if the initial guess is incorrect or if there are other significant binding regions on the receptor. The initial position of the ligand is the current location of an uploaded ligand, will not work with smiles.

If checked / true, uses smina to only calculate the score and minimized score of a provided ligand pose. Output ligand will be near identical to input.

Sets the number of iterations for the steepest descent energy minimization. Energy minimization is a process where the positions of the ligand's atoms are adjusted to reduce the overall energy of the system, leading to a more stable and realistic conformation. This option specifies the number of iterations to perform. The default value (leave as 0) scales with the number of rotatable bonds (rotors) in the ligand, but it may not always be sufficient for full convergence to the lowest energy state. By specifying a higher number of iterations, you can ensure a more thorough minimization, leading to a more optimized and stable ligand conformation.