Hi Sing --

Have you checked to see whether this binding cavity is solvent exposed?  For example, have you used "write dx dielx..." or similar (see http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#write) in an APBS calculation and visualized the resulting map to see if this region of the molecule is really solvent exposed in the APBS calculation?



On Mon, Dec 29, 2008 at 7:54 PM, Kin Sing Stephen Lee <sing@chemistry.msu.edu> wrote:
Dear all,

I have a question about out the parameter of apbs regarding the
electrostatic potential calculation.

I am trying to calculate the electrostatic potential of the binding
pocket. The binding pocket is very hydrophobic and almost totally
embedded inside the protein. So the question is when I set up the
APBS calculation should I still consider the binding pocket have the
dielectric constant of 80 or 2?
If I should set it at 2 is there any possible way that I can restrict
the binding pocket has a dielectric constant of 2 but outside the
protein is 80?

Thank you very much


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Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/