getting .params file for a ligand composed of protein and lipid

Hi all,

 I have a ligand which is composed of protein+lipid and it is a big molecule(please see the attachment). How can I use molfile_to_params.py and get a .params file?  I tried it once, but it gave me several .params and several pdb files as output which I believe it is not right.

I highly appreciate your help.

Thank you