Hello --

1. The tutorial script on protein-protein binding calculates the electrostatic free energy of binding (dG) by subtracting the energies of the individual proteins in water from that of the complex: 
This seems right and simple. However, I've seen in the literature other binding calculations, in which each of the above energies (protein A, protein B, complex) is calculated first as a dG, i.e. in relation to a vacuum reference state:
ddG=dG(complex[water] - complex[vacuum]) - dG(A[water] - A[vacuum]) - dG(B[water] - B[vacuum]).
Are these equivalent?

Yes, if the calculations are converged with respect to grid spacing (e.g., changing the grid spacing no longer changes the answer).

If not, which of the two calculations would you consider more realistic physically/thermodynamically?

In general, the first approach seems to usually be a bit more robust with respect to coarser grid spacings -- but this can be application-dependent.

2. Does anybody have a script which combines polar and apolar APBS calculations (either solvation or binding)? I seem to be able to do them separately but not at the same run.

Really?  What sort of failure are you encoutering?  Can you send an example case that doesn't allow you to combine the two along with the output/error messages?




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Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis