Generating and Displaying an Electostatic Surface

Programs Required

• Pymol http://pymol.sourceforge.net/
• APBS http://sourceforge.net/projects/apbs/ this may require a linux box (or can install via Cygwin)

Generate PQR and PX Files for the Structure

1. Download or generate PDB file.
2. Go to the PDB2PQR server at http://pdb2pqr-1.wustl.edu/pdb2pqr/. The default settings (AMBER forcefield, internal naming scheme) are ok. Check off the Create an APBS input file button.
3. Save the pqr file and the APBS input file.
4. Run APBS as apbs inputfile.in. This will generate a *.dx file.

Visualizing Electrostatic Surface

1. Open pdb file then dx file in pymol.
2. Go to plugin -> apbs tools -> visualization.
3. Go to the visualization tab.
4. Under molecular surface click Color by potential on sol. accesible surface.
5. Click on show and adjust settings to -10kV to 10kV and press show again. You may need to adjust these settings again depending on the charge state of your molecule..