Efficient and accurate methodologies to compute solvation free energies of small molecules are relevant for many biological and industrial research areas including rational drug design. We test the performance of a recently developed Generalized Born method, GB_NSR6 on a common benchmark set of 504 small molecules. The computed solvation energies are compared with those obtained previously by explicit solvent models and experiment. GB_NSR6 offers a reasonable balance between efficiency and accuracy: RMS deviation from experiment of computed solvation energies is 1.2 kcal/mol, which is essentially the same as the accuracy of the much more computationally expensive explicit solvent treatment. Moreover, our results show that a rigorous comparison between GB and PB solvation energies requires a careful consideration of the solvent/solute dielectric boundary. This issue is important for testing the accuracy of GB flavors as they are often compared against the  PB reference.

Efficient computation of the total solvation energy of small molecules via R6 generalized Born model

244th National Meeting (2012)

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