Re: [apbs-users] potental interpretation if epsilon_mol=epsilon_solvent
Biomolecular electrostatics software
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From: Baker, N. <Nat...@pn...> - 2012-09-28 22:50:52
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Hello -- It would provide a coarse electrostatics description inside the molecule but, if that's all you wanted, then you could just use Coulomb's law. The most useful thing you can do with the results of the calculation you describe is to subtract it from the results of a heterogeneous dielectric calculation (e.g., solvent dialectic 80, solute dielectric 2). The resulting potential will be the reaction field potential attributable to the polarization of the solvent around the solute. Thanks, -- Nathan Baker Pacific Northwest National Laboratory Tel: +1-509-375-3997 http://nabaker.me From: "M.V...@lu...<mailto:M.V...@lu...>" <M.V...@lu...<mailto:M.V...@lu...>> Date: Friday, September 28, 2012 7:25 AM To: APBS-USERS mailing list <apb...@li...<mailto:apb...@li...>> Cc: APBS-USERS mailing list <apb...@go...<mailto:apb...@go...>> Subject: [apbs-users] potental interpretation if epsilon_mol=epsilon_solvent Dear, how should I interpret the final potential that I got from APBS after setting the dielectric constant of the solvent equal to the dielectric constant of the solute =2? Would this give me a course representation of the potential inside the molecule due to redistribution of the charges via e.g. covalent bonds (if initially AMBER force field is used in pdb2pqr)? Is this redistribution between a small groups of atoms (residues). thank you a lot M Vulovic TU Delft/LUMC |