I calculated the coulombic surface and the electrostatic surface for my molecule. They show a significant difference in the shape of a small surface area. For the electrostatic surface, I converted the pdb file into a pqr file using the pdb2pqr called from chimera. Then I ran APBS also from within Chimera. When I display this surface it exhibits a strong protrusion in an area where there is no side chain. This protrusion is not present in the Coulombic surface. Any idea where this is coming from?

Thanks

Ursula

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Ursula Schulze-Gahmen, Ph.D.
Assistant Researcher
UC Berkeley, QB3
356 Stanley Hall #3220
Berkeley, CA 94720-3220