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