Missing bond parameter: SH-SH (atoms 52- 566)
Missing bond parameter: SH-SH (atoms 130- 376)
Missing bond parameter: SH-SH (atoms 301- 519)
Missing angle parameter: C2-SH-SH (atoms 51- 52- 566)
Missing angle parameter: HS-SH-SH (atoms 53- 52- 566)
Missing angle parameter: LP-SH-SH (atoms 55- 52- 566)
Missing dihedral parameter: C2-SH-SH-LP (atoms 51- 52- 566- 569)
Missing dihedral parameter: HS-SH-SH-C2 (atoms 53- 52- 566- 565)
The real problem in this case is
neglecting to replace CYS with the disulfide residue CYX and
then trying to attach SH with SH, which there are no parameters for.