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?

  • 1
    $\begingroup$ I think this will be highly sensible to the protein and the ambient where this membranes are. Could you provide more information about which organism or the ambient of the membrane? $\endgroup$ – llrs Jan 17 '19 at 16:59
  • $\begingroup$ @llrs I've updated the question.What about the membrane type would affect the forcefield? I'm surprised they are that sensitive! $\endgroup$ – James Jan 17 '19 at 17:46
  • $\begingroup$ As a disclaimer I don't know much about protein-structure, but what I know is that the folding of a structure depends on the energy local minimum on a given environment. So the proteins or the structure of the membrane would affect, but take it with a grain of salt $\endgroup$ – llrs Jan 17 '19 at 21:27

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Browse other questions tagged or ask your own question.