Dear Abhishek, If you have PDB2PQR installed, it is easy to generate a pqr file with a pdb containing several chains. You have to ensure your PDB has a different chain ID for all your monomers.
As far as I can tell, on a linux box, use the following command: pdb2pqr.py --ff=(Your choice of Forcefield) --chain --with-ph=(Your choice) input.pdb output.pqr --apbs-input --chain tells pdb2pqr to keep the chain ID record in the pqr file --with-ph is optional if you want to use PROPKA --apbs-input is optional, it will generate an input for APBS you can tweak to your needs. I usually generate the pqr this way (without the --apbs-input option), load the pqr in Pymol and use the APBS plugin. Of course you will need to have APBS installed. Regards, Ludovic.
