MBG wiki: Editing revision 3 of Electrostatics calculations with APBS and PyMol

Editing old revision 3. Saving this page will replace the latest revision with this text.

[[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 <b>/usr/local/bin/psize.py</b> 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).

[[image: Electrostatics with APBS and PyMol (molecular surface)]]

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