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After looking through the Tinker 5 preview source code after Mark Friedrichs noted that the ACE nonpolar contribution to the GBSA force comes from the implementation in Tinker, I see that I am now entirely confused about exactly what you are computing. The Tinker code in fact uses (in 'surface.f') the analytical surface-area calculation strategy in the following references: c ############################################################ #### c ## ## c ## subroutine surface -- accessible surface area & derivs ## c ## ## c ############################################################ #### c c c "surface" performs an analytical computation of the weighted c solvent accessible surface area of each atom and the first c derivatives of the area with respect to Cartesian coordinates c c literature references: c c T. J. Richmond, "Solvent Accessible Surface Area and c Excluded Volume in Proteins", Journal of Molecular Biology, c 178, 63-89 (1984) c c L. Wesson and D. Eisenberg, "Atomic Solvation Parameters c Applied to Molecular Dynamics of Proteins in Solution", c Protein Science, 1, 227-235 (1992) This is *not* the same as the ACE solvent model of Schaefer and Karplus I had presumed Mark was referring to when he stated that OpenMM uses ACE. Could you please clarify exactly what is being computed in the SA portion of the GBSA model, and what parameters are used? This should all be explicitly documented in the API to save other users of the API the headache of trying to figure out exactly what the interface is supposed to implement by trial- and-error. Thanks, John
There was no documentation in the GBSAOBCForce header for how the SASA term was to be calculated, nor a mechanism for setting the SASA penalty, so I asked Mark Friedrichs how this was computed. According to Mark (though I potentially misunderstood what he said), this term is actually the ACE solvent model of Schaefer and Karplus: M. Schaefer & M. Karplus (1996) J. Phys. Chem. 100, 1578-1599. The AMBER GBSA implementation (and what is commonly understood as the 'SA' component of GBSA and PBSA) is a simple solvent accessible surface area based penalty term (often set to 5 cal/mol/A^2). I believe AMBER uses LCPO (linear combination of pairwise overlap) to estimate the SASA, though this approximation is often a poor mimic of the true SASA.
Could you explain what you mean? GBSAOBCForce does include an SASA term.
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