CHARMM Development Project Forums CHARMM Interfaces CHARMM-GUI PDB reading for structure with unresolved loop?

I am trying to use CHARMM-GUI to read a PDB structure (single-chain) that has an unresolved loop. I would like the missing residues to be capped with neutral termini, like this:

AAAAAAAAAAAXXXXXXXXXXXBBBBBB
AAAAAAAAAAA-CT3 ACE-BBBBBB

What CHARMM-GUI returns is this:

AAAAAAAAAAABBBBBB

Is there a simple way to do that?

CHARMM-GUI has to recognize the two chains are separate. I haven't tested, but either
a) you can put "TER" in your PDB file between chain "A" and "B" or
b) rename the chain ID, such that chain "A" and "B" has different chain ID.

Thanks,
Sunhwan

Inserting a "TER" line did the trick. Thanks, Sunhwan!