I docked a ligand into a monomer, now I want to save a new pdb file. In the new pdb file, chian A will be docked monomer, chain B will be the chain B of homodimer. I already superimposed the two PDB files and deleted chain A of homodimer. I also used change chain ID to add chain IDs to the combined PDB file. However I got the following problems:

1. In my system, there are glycans (residue name: 0YB), I cannot add chain ID to the glycans (residue 209-216 belongs to chain A, residue 425-432 belongs to chain B)

2. In my system, I also have a small molecule docked in chain A, I realized only the last line of the ligand was given a chain ID "h", is this a problem?

3. I want to save these two PDB files as two chains, not two models (actually it's a homodimer except for the ligand)

4. Can I manually delete all the connections?

Looking forward to your reply.

Best regards,

Rui