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Center for Nonlinear Studies |
Many biological processes, including enzyme catalysis, particle transfer and ligand binding, are dependent on molecule orientation and molecular electrostatic potential. Because biological systems are too large for full quantum mechanical (QM) simulations, the state of the art for simulating these processes involves representing the "active region" with QM, while the rest of the system is included via a molecular mechanics (MM)potential (QM/MM). The parameters of the MM potentials currently in use have been fitted to pieces of proteins generally in solution, hence they do not include the polarization due to the protein environment. Recently our group developed a novel protocol that allows for the inclusion of these polarization effects in the MM region, leading to more accurate ab initio calculations of the energy landscape of biological molecules.The focus now is to develop a method that allows this protocol to be combined with geometry optimization, thus obtaining the mo! st accurate charges and geometry for the molecule of interest. This combination should allow for more accurate simulations of biological processes.