ヤマモト　ノリフミ   Norifumi Yamamoto   山本　典史    所属   千葉工業大学  工学部 応用化学科    千葉工業大学  工学研究科 工学専攻    千葉工業大学  工学研究科 応用化学専攻    職種   教授
言語種別	日本語
発行・発表の年月	2013
形態種別	学術雑誌
査読	査読あり
標題	A Minimal Implementation of the AMBER-PAICS Interface for Ab Initio FMO-QM/MM- MD Simulation
執筆形態	共著
掲載誌名	Bulletin of the Chemical Society of Japan
巻・号・頁	86,210-222頁
著者・共著者	Takuya Okamoto, Takashi Ishikawa, Yoshiyuki Koyano, Norifumi Yamamoto, Kazuo Kuwata, Masataka Nagaoka
概要	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