The CHARMM additive forcefield (current version 36) is really just ONE forcefield, which for practical reasons is contained in a small set of component files, which are all fully compatible with each other. You simply read the files that your application requires - if you are unsure you could read them all.

Similarly the polarizable version is ONE forcefield, with a number of mutually compatible components.

So, yes, you can (and should) read the potein and nucleic acid files AS THEY ARE.

Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden