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Hybrid Quantum Mechanics/Molecular Mechanics/Coarse Grained Modeling: A Triple-Resolution Approach for Biomolecular Systems

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Sokkar,  Pandian
Research Group Sánchez-García, Max-Planck-Institut für Kohlenforschung, Max Planck Society;

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Boulanger,  Eliot
Research Department Thiel, Max-Planck-Institut für Kohlenforschung, Max Planck Society;

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Thiel,  Walter
Research Department Thiel, Max-Planck-Institut für Kohlenforschung, Max Planck Society;

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Sanchez-Garcia,  Elsa
Research Group Sánchez-García, Max-Planck-Institut für Kohlenforschung, Max Planck Society;

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ct500956u_si_001.pdf
(Supplementary material), 297KB

Citation

Sokkar, P., Boulanger, E., Thiel, W., & Sanchez-Garcia, E. (2015). Hybrid Quantum Mechanics/Molecular Mechanics/Coarse Grained Modeling: A Triple-Resolution Approach for Biomolecular Systems. Journal of Chemical Theory and Computation, 11(4), 1809-1818. doi:10.1021/ct500956u.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0026-BBCB-D
Abstract
We present a hybrid quantum mechanics/molecular mechanics/coarse-grained (QM/MM/CG) multiresolution approach for solvated biomolecular systems. The chemically important active-site region is treated at the QM level. The biomolecular environment is described by an atomistic MM force field, and the solvent is modeled with the CG Martini force field using standard or polarizable (pol-CG) water. Interactions within the QM, MM, and CG regions, and between the QM and MM regions, are treated in the usual manner, whereas the CG–MM and CG–QM interactions are evaluated using the virtual sites approach. The accuracy and efficiency of our implementation is tested for two enzymes, chorismate mutase (CM) and p-hydroxybenzoate hydroxylase (PHBH). In CM, the QM/MM/CG potential energy scans along the reaction coordinate yield reaction energies that are too large, both for the standard and polarizable Martini CG water models, which can be attributed to adverse effects of using large CG water beads. The inclusion of an atomistic MM water layer (10 Å for uncharged CG water and 5 Å for polarizable CG water) around the QM region improves the energy profiles compared to the reference QM/MM calculations. In analogous QM/MM/CG calculations on PHBH, the use of the pol-CG description for the outer water does not affect the stabilization of the highly charged FADHOOH-pOHB transition state compared to the fully atomistic QM/MM calculations. Detailed performance analysis in a glycine–water model system indicates that computation times for QM energy and gradient evaluations at the density functional level are typically reduced by 40–70% for QM/MM/CG relative to fully atomistic QM/MM calculations.