On Fri, Apr 26, 2013, Sun wrote:
> I wander what is the role of surface charge in the MMPBSA calculation
> of binding free energy ? Here is a specific example: in the output file
> of a MMPBSA calculation, there are 3 terms being recorded in terms of
> Total surface charge,Reaction field energy and Cavity solvation energy
> corresponding to complex,receptor and ligand, respectively. But the
> Gsolv energy of complex (or receptor and ligand ) equals the sum of
> Reaction field energy plus Cavity solvation energy, it seems that the
> surface charge has nothing to do with the calculation . So I want to
> know where the surface charge is used in the MMPBSA calculation ?
The surface charges are an intermediate set of numbers, used to help
convergence in the calculation of the reaction field. Seeing the total
surface charge can be helpful in identifying errors (it should be
-(1 - 1/eps) * system charge, generally), but is not directly used in
computing free energies.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 26 2013 - 18:00:02 PDT
