I am trying to model a 2-chain Ab sequence, but I keep getting the
same error. I think it is not reading the chain break '/' correctly,
but not sure.
You have your chains the wrong way round.
You have asked Modeller to read everything from the start of the H chain
to the end of the L chain, but Modeller simply reads residues as they
are presented to it in the PDB, and 1u6a has the L chain *before* the H
chain. So Modeller happily skips all of the L chain to find residue 2:H
before it starts reading, and then it reads all the way to the end of
the H chain before stopping (since it never finds 215:L). Either swap
the chains in your alignment file, or edit the PDB file to put them in
the desired order.