Flexible effective fragment QM/MM method: Validation through the challenging tests
- 8 July 2003
- journal article
- research article
- Published by Wiley in Journal of Computational Chemistry
- Vol. 24 (12) , 1410-1420
- https://doi.org/10.1002/jcc.10309
Abstract
A new version of the QM/MM method, which is based on the effective fragment potential (EFP) methodology [Gordon, M. et al., J Phys Chem A 2001, 105, 293] but allows flexible fragments, is verified through calculations of model molecular systems suggested by different authors as challenging tests for QM/MM approaches. For each example, the results of QM/MM calculations for a partitioned system are compared to the results of an all‐electron ab initio quantum chemical study of the entire system. In each case we were able to achieve approximately similar or better accuracy of the QM/MM results compared to those described in original publications. In all calculations we kept the same set of parameters of our QM/MM scheme. A new test example is considered when calculating the potential of internal rotation in the histidine dipeptide around the CαCβ side chain bond. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1410–1420, 2003Keywords
This publication has 41 references indexed in Scilit:
- Study of the Opsin Shift of Bacteriorhodopsin: Insight from QM/MM Calculations with Electronic Polarization Effects of the Protein EnvironmentThe Journal of Physical Chemistry B, 2001
- Mixedab initio QM/MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptideJournal of Computational Chemistry, 1999
- Adjusted Connection Atoms for Combined Quantum Mechanical and Molecular Mechanical MethodsThe Journal of Physical Chemistry A, 1999
- A Generalized Hybrid Orbital (GHO) Method for the Treatment of Boundary Atoms in Combined QM/MM CalculationsThe Journal of Physical Chemistry A, 1998
- Catalytic Mechanism of the Enzyme Papain: Predictions with a Hybrid Quantum Mechanical/Molecular Mechanical PotentialJournal of the American Chemical Society, 1997
- Quantum chemical computations on parts of large molecules: the ab initio local self consistent field methodChemical Physics Letters, 1996
- An examination of a density functional/molecular mechanical coupled potentialJournal of Computational Chemistry, 1995
- Free energy perturbation method for chemical reactions in the condensed phase: a dynamic approach based on a combined quantum and molecular mechanics potentialJournal of the American Chemical Society, 1987
- A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl + Cl− exchange reaction and gas phase protonation of polyethersJournal of Computational Chemistry, 1986
- Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozymeJournal of Molecular Biology, 1976