{"title":"Large-Scale FMO-MP2 Calculations of the Spike Protein Droplet Model","authors":"Hideo Doi, Tatsuya Nakano, Kota Sakakura, Kazuki Akisawa, Koji Okuwaki, Yoshinori Hirano, Eiji Yamamoto, Kenji Yasuoka, Satoshi Ohshima, Takahiro Katagiri, Yuji Mochizuki","doi":"10.1002/jcc.70052","DOIUrl":null,"url":null,"abstract":"<p>The spike protein of SARS-CoV-2 is a challenging target for theoretical approaches. Here we report a benchmark calculation of the spike protein droplet model by the fragment molecular orbital (FMO) at the second-order Møller-Plesset perturbation (MP2) level on the supercomputer Fugaku. One hundred structure samples from molecular dynamics (MD) simulations were used for both the closed and open forms of this protein (PDB IDs 6XLU and 6XM0 respectively). The number of total fragments is about 20,000, and the job time per structure was about 2 h on 8 racks of Fugaku.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 4","pages":""},"PeriodicalIF":3.4000,"publicationDate":"2025-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70052","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Computational Chemistry","FirstCategoryId":"92","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1002/jcc.70052","RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"CHEMISTRY, MULTIDISCIPLINARY","Score":null,"Total":0}
引用次数: 0
Abstract
The spike protein of SARS-CoV-2 is a challenging target for theoretical approaches. Here we report a benchmark calculation of the spike protein droplet model by the fragment molecular orbital (FMO) at the second-order Møller-Plesset perturbation (MP2) level on the supercomputer Fugaku. One hundred structure samples from molecular dynamics (MD) simulations were used for both the closed and open forms of this protein (PDB IDs 6XLU and 6XM0 respectively). The number of total fragments is about 20,000, and the job time per structure was about 2 h on 8 racks of Fugaku.
期刊介绍：
This distinguished journal publishes articles concerned with all aspects of computational chemistry: analytical, biological, inorganic, organic, physical, and materials. The Journal of Computational Chemistry presents original research, contemporary developments in theory and methodology, and state-of-the-art applications. Computational areas that are featured in the journal include ab initio and semiempirical quantum mechanics, density functional theory, molecular mechanics, molecular dynamics, statistical mechanics, cheminformatics, biomolecular structure prediction, molecular design, and bioinformatics.
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