[apbs-users] pKA

[chemocev marker]

Hi

I am just calculating the Electrostatic Potential, and I wanted to know your opinion which force field is better for metallo proteins.And what is criteria to choose and not to choose the pKA...

As I am doing the reaction at different pH and what I see in the PDB the proteins are crystallized at different PhD then the reaction conditions. Structures are solved at low pH but the reactions are done at high pH.

best

Jiri

[Baker, Nathan]

Hello –

 

I am not aware of a force field that has been specifically developed for implicit solvent electrostatics calculations on metalloproteins.  If you are interested in very coarse-grained calculations, it is probably sufficient to use existing force fields.  Otherwise, you will need to develop your own charge parameters to use with existing radii parameter sets (e.g., AM1-BCC charges with the ZAP radii).

 

Thank you,

 

-- 

Nathan Baker

Advanced Computing, Mathematics, and Data Division — Pacific Northwest Natl Lab

Division of Applied Mathematics — Brown University

+1-509-375-3997 — http://go.usa.gov/xWY9Y