How do I get the electrostatic surface potential for a certain structure?
Sources; [25] • See APBS tutorial • Use PyMol: Pymol can generate the potential map for you while displaying the potential spectrum of your protein. Steps: • Load your PDB file ‘your.pdb’ into PyMol • From the main menu choose Plugin -> APBS tools • Click ‘Use another PQR’ and click ‘Choose Externally Generated PQR:’ to load the pqr you just generated by pdb2pqr program (your.pqr). You can also go to the ‘Configuration’ tab to set your environment such as temp, dielectrics, etc.
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