Dear Nathan,

In my case, it is a little bit different because my ligand is covalently bonded with the protein and I don't have the parameter of the ligand so I just delete the ligand from the crystal structure so I don't know how to set up the apbs calculation with thise case. But the binding pocket should not be solvent exposed. 

Thank you 

Sing

On Dec 30, 2008, at 11:39 AM, Nathan Baker wrote:

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?

Thanks,

Nathan

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

Sing


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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/