- 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
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.