The generalized molecular fractionation with conjugate caps/molecular mechanics method for direct calculation of protein energy

Xiao He, John Zhang

Research output: Contribution to journalArticle

Abstract

A generalized molecular fractionation with conjugate caps/molecular mechanics (GMFCC/MM) scheme is developed for efficient linear-scaling quantum mechanical calculation of protein energy. In this GMFCC/MM scheme, the interaction energy between neighboring residues as well as between non-neighboring residues that are spatially in close contact are computed by quantum mechanics while the rest of the interaction energy is computed by molecular mechanics. Numerical studies are carried out to calculate torsional energies of six polypeptides using the GMFCC/MM approach and the energies are shown to be in general good agreement with the full system quantum calculation. Among those we tested is a polypeptide containing 396 atoms whose energies are computed at the MP26-31 G* level. Our study shows that using GMFCC/MM, it is possible to perform high level ab initio calculation such as MP2 for applications such as structural optimization of protein complex and molecular dynamics simulation.

Original languageEnglish (US)
Article number184703
JournalJournal of Chemical Physics
Volume124
Issue number18
DOIs
StatePublished - 2006

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Molecular mechanics
Fractionation
caps
fractionation
proteins
Proteins
polypeptides
energy
Peptides
Structural optimization
Quantum theory
Molecular dynamics
quantum mechanics
Atoms
interactions
molecular dynamics
Computer simulation
scaling
optimization
atoms

ASJC Scopus subject areas

  • Atomic and Molecular Physics, and Optics

Cite this

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abstract = "A generalized molecular fractionation with conjugate caps/molecular mechanics (GMFCC/MM) scheme is developed for efficient linear-scaling quantum mechanical calculation of protein energy. In this GMFCC/MM scheme, the interaction energy between neighboring residues as well as between non-neighboring residues that are spatially in close contact are computed by quantum mechanics while the rest of the interaction energy is computed by molecular mechanics. Numerical studies are carried out to calculate torsional energies of six polypeptides using the GMFCC/MM approach and the energies are shown to be in general good agreement with the full system quantum calculation. Among those we tested is a polypeptide containing 396 atoms whose energies are computed at the MP26-31 G* level. Our study shows that using GMFCC/MM, it is possible to perform high level ab initio calculation such as MP2 for applications such as structural optimization of protein complex and molecular dynamics simulation.",
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