I am generating PQR files for a membrane protein that is almost entirely buried in the membrane. There are no lipids in the structure.
PDB2PQR has predefined options of amber, charmm, parse, tyl06, peoepb and swanson. It also allows user supplied forcefields.
The protein is an ion channel in the plasma membrane of a human. I'll be processing in memAPBS. However, I would greatly appreciate a "rule of thumb" answer as I plan to use the same method on TMPs from other organisms in various subcellular membranes.
What is a sensible forcefield choice for membrane proteins when generating PQR files for electrostatic analysis?