Electrostatics calculations with APBS and PyMol

APBS is available on all machines but PyMol is only available on the newer nodes. You better sit on one of them.

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Start with a clean PDB of your structure. PyMol can add missing hydrogens and side chains (?), but you can always use a PDB file prepared by psfgen. Then :

• pymol mypdb.pdb
• Plugin → APBS tools
• Select APBS Location. The APBS binary location should already be there (/usr/local/bin/apbs). Add the location of the psize.py file by typping /usr/local/bin/psize.py in the box labeled as such.
• Click 'Set grid' at the bottom of the APBS tools window.
• The unix shell should inform you of the grid size for the calculation.
• Click 'Run APBS' at the bottom of the APBS tools window.
• Select Visualization and click Update. The sub-menus for molecular surface, and the two isosurfaces should appear.
• Click Update in the 'Molecular Surface' sub-menu. You should see it.
• You can also try to plot the isosurfaces (with the 'update' switch in their respective submenus).