Sorry, your question is very vague and I’m not sure I understood what you meant
In the initial pdb file the protein consists of two chains A and B
So you have two molecules with 3 chains? Which chains from which molecule do you want do use for docking?
Supposing that you have:
Molecule 1: Chain A, Chain B
Molecule 2: Chain A
And you want to use all chains of Molecule 1, on the field
Which chain of the structure must be used? you’d select
All, if you just want to use chain A, you’d select
By default Molecule 1 will become segid A, Molecule 2 segid B, Molecule 3 segid C, so on and so forth. Now, if you want your resulting complex to reflect the same chain ids of your input, you need to change it yourself. Please have a look at PDB-Tools or else you can just write a simple script to handle the renaming of the chains based on your input.