generate proper characters of ion channel embeded in a membrane

[linda091021]

Dear all,
How could I get the proper electric charge and electrostatic potential of an ion channel through PDB2PQR and APBS.
I did't notice any options to set a membrane environment on this server https://server.poissonboltzmann.org/.

or the electric charge is not influenced by the environment? The .pqr file generated is all right?

In that case, how could I generate a membrane environment to calculate electrostatic potential of an ion channel, which should be definitely influenced by solvent or membrane. I did't find any options in the server or plugin in PyMOL.

At this moment, I generate the electrostatic potential through plugin in PyMOL.
As there is a pore in the center of the ion channel, if I only focus on the electrostatic potential of this pore region, could I think the results around the pore region is reliable?
I'm wondering if the pore region is considered full of solvent with dielectric constant=2 in the APBS calculation, even if I hadn't defined a cylinder region to represent the pore region?

Thanks!

[sobolevnrm]

Hello --

I'm sorry but we do not currently have automatic options for setting up membrane environments around a protein as part of the main APBS package. However, Michael Grabe has developed the APBSmem package which may do something very similar to what you're asking.

Thank you,

Nathan

[linda091021]

Hi, Nathan

Thank you so much for the kind suggestions and quick reply!

I'll try the the APBSmem package you mentioned.

Best Wishes!

Linlin