Computational Methods for Biochemical Simulations Implemented in GAMESS

Dmitri G. Fedorov, Hui Li, Vladimir Mironov, Yuri Alexeev

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Computational methods for modeling biochemical processes implemented in GAMESS package are reviewed; in particular, quantum mechanics combined with molecular mechanics (QM/MM), semi-empirical, and fragmentation approaches. A detailed summary of capabilities is provided for the QM/MM implementation in QuanPol program and the fragment molecular orbital (FMO) method. Molecular modeling and visualization packages useful for biochemical simulations with GAMESS are described. GAMESS capabilities with corresponding references are tabulated for reader's convenience.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages123-142
Number of pages20
DOIs
StatePublished - 2020

Publication series

NameMethods in Molecular Biology
Volume2114
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Keywords

  • Fragment molecular orbital (FMO)
  • GAMESS
  • GUI
  • Molecular mechanics (MM)
  • QuanPol
  • Quantum mechanics (QM)

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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