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Intraprotein electrostatics derived from first principles: Divide-and-conquer approaches for QM/MM calculations
Article first published online: 23 SEP 2003
DOI: 10.1002/jcc.10333
Copyright © 2003 Wiley Periodicals, Inc.
1096-987X/asset/cover.gif?v=1&s=4429aac2462ebd499c13b3d7fe983679c5767778 "Journal of Computational Chemistry")
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How to Cite
Molina, P. A., Li, H. and Jensen, J. H. (2003), Intraprotein electrostatics derived from first principles: Divide-and-conquer approaches for QM/MM calculations. Journal of Computational Chemistry, 24: 1971–1979. doi: 10.1002/jcc.10333
Publication History
- Issue published online: 23 SEP 2003
- Article first published online: 23 SEP 2003
- Manuscript Accepted: 22 APR 2003
- Manuscript Received: 17 MAR 2003
Funded by
- Research Innovation Award from the Research Corporation and the National Science Foundation. Grant Number: MCB 0209941
- NSF. Grant Number: CHE-9974502
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Graphical Abstract
Abstract
Two divide-and-conquer (DAQ) approaches for building multipole-based molecular electrostatic potentials of proteins are presented and evaluated for use in QM/MM calculations. One approach is a further development of the neutralization method of Bellido and Rullmann (J Comput Chem 1989, 10, 479–487) while the other is based on removing part of the electron density before performing the multipole expansion. Both methods create systems with integer charges without using charge renormalization. To determine their performance in terms of location of cuts and distance to QM region, the new DAQ approaches are tested in calculations of the proton affinity of Nζ of Lys55 in the inhibitor turkey ovomucoid third domain. Finally, the two methods are used to build a variety of MM regions, applied to calculations of the pKa of Lys55, and compared to other computational methodologies in which force field charges are employed. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1971–1979, 2003