Forcefield typing

Hi all

I have a protein 1LTE, whose biological unit has two conformers. I want to run a simulation job by applying the distance constraints. I followed the below steps

1. i converted the conformers to molecules

2. changed the chains IDS, since both the conformer had the same ID

3. Typed the complete molecule using charmm.

when i clicked on protein groups in the hierarchial pane, it was highlighting only a few regions in the protein, but the whole protein was not highlighted. Moreever when i clicked on the more button in forcefield typing, it was showing a list of residues [known amino acids] not been typed. what could be the reason