Diogo

I think you want to use option "--scoring ad4" with vina.

1. i agree 2. if the energies are positive it is possible that the box is too small 3. see the python docs in the vina readthedocs page

See "Why do I not get the correct bound conformation?" in https://autodock-vina.readthedocs.io/en/latest/faq.html for some pointers. To that I'll add keeping/removing water molecules, and note that meeko+vina can sample macrocycles but...

1. There's a lot of literature on this topic, for example: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4437766/ https://jcheminf.biomedcentral.com/articles/10.1186/1758-2946-6-12 2. No, autodock4 can't sample small rings either.

For people to be able to help you, you need to provide more detailed information: 1. exact vina command and all input files to reproduce the problem. You posted only...

Then it's running. But with that many sidechains, it just takes extremely long. Molecular viewers show gaps because the protein is split between different files, but all atoms should be...

Possibly. But not as fast as having fewer sidechains.

The vina scoring function, which is the default (e.g., `v = Vina()`), handles metals. There's zinc specific potentials but that is for the autodock4 scoring function.

Can you post the gpf contents?

Thanks. Do you know of an actual conflict or is it just to prevent a possible conflict?