Thanks for pointing this out, I tried to look for a new site but could not find anything - we’ll reach out to them and ask if where the domain has moved.
Each of these files describe different things so that CNS (the molecular engine used by Haddock) can interpret the molecule; the topology represents what are the atomic types and their properties (mass, charge), the parameters are a description of the values that should be used for the inter and intra-molecular calculations, the pdb itself described the spatial cordinates of the atoms. So indeed you need all of them.
Yes they should! I’ve updated the server so that once you click the Download input files, you will also get the PRODRG generated topologies and parameters. From there what you need to do is feed these files into your toml configuration for haddock3:
ligand_param_fname = "/path/to/the/data/ligand.par"
ligand_top_fname = "/path/to/the/data/ligand.top"
You can use this docking-protein-ligand-full.toml as a template for your setup.
Good luck!