This simple file describes reading and writing a PDB with Rosetta Run it like this: "readAndWritePDB.cc -in::file::s <PDB file name> -in::path::database <database root dir>"

If you provide a PDB with a ligand that has multiple residues, this code will "glue" them together Of course you would need to provide information about these additional residues: in::file::extra_res_fa <list of extra params files, one per residue type>