A Minimal Implementation of the AMBER-PAICS Interface for Ab Initio FMO-QM/MM-MD Simulation

• Takuya Okamoto

  Graduate School of Information Science, Nagoya University

• Takeshi Ishikawa

  Division of Prion Research, Center for Emerging Infectious Disease, Gifu University

• Yoshiyuki Koyano

  Graduate School of Information Science, Nagoya University

• Norifumi Yamamoto

  Graduate School of Information Science, Nagoya University

• Kazuo Kuwata

  Division of Prion Research, Center for Emerging Infectious Disease, Gifu University

• Masataka Nagaoka

  Graduate School of Information Science, Nagoya University

Abstract

For the purpose of providing a realistic description of the reaction mechanisms in large molecular systems, we propose a quantum mechanical/molecular mechanical (QM/MM) method combined with the ab initio fragment molecular orbital (FMO) method, i.e., the ab initio FMO-QM/MM method. By connecting a molecular dynamics (MD) program AMBER with an FMO program PAICS, we have implemented an AMBER-PAICS interface (AP-IF). Using the AP-IF, we demonstrate three example applications: (a) a hydrogen fluoride and water molecular clusters, (b) an alanine dipeptide in aqueous solution, and (c) a prion protein–GN8 complex. From these results, it is confirmed that the FMO-QM/MM method offers a good compromise between chemical accuracy and computational cost and enables us to obtain in ab initio quality the inter- and intramolecular interaction energies between molecules or residues in large molecular systems such as solution and biomolecule, by using the dynamics-based interfragment interaction energy (IFIE) analysis.

Journal

• Bulletin of the Chemical Society of Japan

  Bulletin of the Chemical Society of Japan 86 (2), 210-222, 2013-02

  Oxford University Press (OUP)

Keywords

• General Chemistry

Details

• CRID: 1360846644027008768
• NII Article ID: 10031155742
• NII Book ID: AA00580132
• DOI: 10.1246/bcsj.20120216
• ISSN: 13480634
• ISSN: 00092673
• Web Site: https://academic.oup.com/bcsj/article-pdf/86/2/210/56275039/bcsj.20120216.pdf
• Data Source:
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