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Can I obtain the breakdown of the electrostatic contributions to pK into the “Born” (desolvation penalty) and “Background” terms?

April 26, 2017background born breakdown contributions electrostatic obtain penalty pk terms

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Can I obtain the breakdown of the electrostatic contributions to pK into the “Born” (desolvation penalty) and “Background” terms?

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Yes. These are in the “your_molecule.summ” file. See the above. A very detailed decomposition of the energetic contributions to pK from every residue is available from “your_molecule.pK_decomposition” References: Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., and Simmerling, C. (2006). Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins: Structure, Function, and Bioinformatics, Vol. 65, No. 3, pp. 712-725. Perez, A., Marchan, I., Svozil, D., Sponer, J., Cheatham, T.E., Laughton, C.A., and Orozco, M. (2007). Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of alpha/gamma Conformers. Biophys. J., Vol. 92, No. 11, pp. 3817-3829. Wang, J., and Kollman P.A. (2001). Automatic parameterization of force field by systematic search and genetic algorithms. Journal of Computational Chemistry, Vol. 22, No. 12, pp. 1219-1228.