I have a structure for a membrane protein and I wish to visualize the electrostatic potential taking into consideration the lipid bilayer. I first ran PDB2PQR from the command line. Then I ran APBS with draw_membrane2 via my edited Run_membrane-helix.sh file.
I have two questions.
(1) How can I resolve the following warning:
Warning: The 'nlev' keyword is now deprecated!
(2) Other than the warning above, output gives me a Global net ELEC energey=1.77 kJ/mol, several *.dx files, io.mc, and a *_solv.out file. How can I use the output from APBS run from the terminal to view the surface charge and membrane section in PYMOL or VMD?
Department of Molecular Biology & Biochemistry