Electrostatically embedded generalized molecular fractionation with conjugate caps method for full quantum mechanical calculation of protein energy

Xianwei Wang, Jinfeng Liu, John Zhang, Xiao He

Research output: Contribution to journalArticle

Abstract

An electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method is developed for efficient linear-scaling quantum mechanical (QM) calculation of protein energy. This approach is based on our previously proposed GMFCC/MM method (He; et al. J. Chem. Phys. 2006, 124, 184703), In this EE-GMFCC scheme, the total energy of protein is calculated by taking a linear combination of the QM energy of the neighboring residues and the two-body QM interaction energy between non-neighboring residues that are spatially in close contact. All the fragment calculations are embedded in a field of point charges representing the remaining protein environment, which is the major improvement over our previous GMFCC/MM approach. Numerical studies are carried out to calculate the total energies of 18 real three-dimensional proteins of up to 1142 atoms using the EE-GMFCC approach at the HF/6-31G* level. The overall mean unsigned error of EE-GMFCC for the 18 proteins is 2.39 kcal/mol with reference to the full system HF/6-31G* energies. The EE-GMFCC approach is also applied for proteins at the levels of the density functional theory (DFT) and second-order many-body perturbation theory (MP2), also showing only a few kcal/mol deviation from the corresponding full system result. The EE-GMFCC method is linear-scaling with a low prefactor, trivially parallel, and can be readily applied to routinely perform structural optimization of proteins and molecular dynamics simulation with high level ab initio electronic structure theories.

Original languageEnglish (US)
Pages (from-to)7149-7161
Number of pages13
JournalJournal of Physical Chemistry A
Volume117
Issue number32
DOIs
StatePublished - Aug 15 2013

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Fractionation
caps
fractionation
proteins
Proteins
energy
scaling
Structural optimization
Electronic structure
Density functional theory
Molecular dynamics
perturbation theory
fragments
molecular dynamics
density functional theory
electronic structure
deviation
Atoms
optimization
Computer simulation

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

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Electrostatically embedded generalized molecular fractionation with conjugate caps method for full quantum mechanical calculation of protein energy. / Wang, Xianwei; Liu, Jinfeng; Zhang, John; He, Xiao.

In: Journal of Physical Chemistry A, Vol. 117, No. 32, 15.08.2013, p. 7149-7161.

Research output: Contribution to journalArticle

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