By Keith James Laidler
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19(12), 2558–2562. 5. , Riley, K. , and Vondr´aˇsek, J. (2009). Representative amino acid side chain interactions in proteins. A comparison of highly accurate correlated ab initio quantum chemical and empirical potential procedures, J. Chem. Theory Comput. 5, 982–992. 6. Case, D. , Darden, T. , Cheatham III, T. , Simmerling, C. , Duke, R. , Walker, R. , Merz, K. , ¨ A. , Gotz, Wong, K. , Wolf, R. , Brozell, S. , Roe, D. , Mathews, D. , Seetin, M. , R. , and Kollman, P. A. (2012). AMBER 12, University of California, San Francisco, San Francisco, CA.
In addition, we discuss our work on using X-Pol as a quantum mechanical force field (QMFF) for liquid water simulations. 2 Theoretical Background In X-Pol, a macromolecular system is partitioned into molecular fragments, which may be called monomers. , the 02-Qiang-Cui-c02 January 27, 2016 13:7 PSP Book - 9in x 6in 02-Qiang-Cui-c02 Theoretical Background 37 subsystem included in one fragment does not appear in another monomer). 77, 102 Several peptide units can be combined into the same fragment, if desired, which can be useful for modeling systems containing disulfide bonds.
19. Giese, T. , and York, D. M. (2008). Contracted auxiliary Gaussian basis integral and derivative evaluation, J. Chem. Phys. 128(6), 064104. 20. Giese, T. , and York, D. M. (2008). Extension of adaptive tree code and fast multipole methods to high angular momentum particle charge densities, J. Comput. Chem. 29(12), 1895–1904. 21. Giese, T. , and York, D. M. (2008). Spherical tensor gradient operator method for integral rotation: A simple, efficient, and extendable alternative to Slater–Koster tables, J.