著者

林 幸史 岡本 卓也 藤原 武弘 Yoshifumi Hayashi Takuya Okamoto Takehiro Fujihara

雑誌

関西学院大学社会学部紀要 (ISSN:04529456)

巻号頁・発行日

no.106, pp.15-26, 2008-10-30

著者

岡本 卓也 藤原 武弘 Takuya Okamoto Takehiro Fujihara

雑誌

関西学院大学社会学部紀要 (ISSN:04529456)

巻号頁・発行日

no.120, pp.167-180, 2015-03-15

著者

Takuya Okamoto Takeshi Ishikawa Yoshiyuki Koyano Norifumi Yamamoto Kazuo Kuwata Masataka Nagaoka

出版者

(社)日本化学会

雑誌

Bulletin of the Chemical Society of Japan (ISSN:00092673)

巻号頁・発行日

vol.86, no.2, pp.210-222, 2013-02-15 (Released:2013-02-15)

参考文献数

95

被引用文献数

20 4

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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.