Computational Methods for Biochemical Simulations Implemented in GAMESS

Dmitri G Fedorov; Hui Li; Vladimir Mironov; Yuri Alexeev

doi:10.1007/978-1-0716-0282-9_8

Computational Methods for Biochemical Simulations Implemented in GAMESS

Methods Mol Biol. 2020:2114:123-142. doi: 10.1007/978-1-0716-0282-9_8.

Authors

Dmitri G Fedorov¹, Hui Li², Vladimir Mironov³, Yuri Alexeev⁴

Affiliations

¹ Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan.
² Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA.
³ Department of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation.
⁴ Argonne Leadership Computing Facility and Computational Science Division, Argonne National Laboratory, Lemont, IL, USA. yuri@anl.gov.

PMID: 32016890
DOI: 10.1007/978-1-0716-0282-9_8

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.

Keywords: Fragment molecular orbital (FMO); GAMESS; GUI; Molecular mechanics (MM); QuanPol; Quantum mechanics (QM).

Publication types

Research Support, U.S. Gov't, Non-P.H.S.
Review

MeSH terms

Drug Discovery / methods*
Molecular Dynamics Simulation
Quantum Theory
Software