I can spot three issues:
A) core.pack.rotamer_set.RotamerSet_: [ WARNING ] including current in order to get at least 1 rotamer !!!!!! 60 cym
This means you have not provided any rotamers for your new residue – I thought you said you were going to make your own rotamer library? I notice there’s no PDB_ROTAMERS line in the params file.
core.mm.MMBondAngleLibrary: No parameters for X-X-C
This is a combination of two problems. The direct problem is that your MMBondAngleLibrary does not have bond angle parameters for that bond. The reason it doesn’t have them is that two of the atoms have MM atom types of “X”. To fix this, you’ll need to edit your params file so that the fourth column in the atom definition lines is a valid MM atom type. The MM atom types are in chemical/mm_atom_type_sets/fa_standard/mm_atom_types; I think they’re from CHARMM, hopefully those files will make it clear. If your ligand has new atom types, you’ll need to add them to the files in that directory and find parameters for them that are consistent with the same forcefield (again, I think it’s CHARMM).
C) “and in the PDB file there was actually e.g C01 C03 C05.. instead of e.g CZ CT1 CT2 in the params file. ” I don’t understand the question – if you don’t like the atom names in the INPUT pdb, then you should change them to match the params file. Is this in relation to an output pdb…?