Development of more accurate molecular dynamics simulation method by combining ab initio all electron calculation method for proteins
| Project/Area Number |
17510156
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
基礎ゲノム科学
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| Research Institution | Hirosaki University |
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Principal Investigator |
SAITO Minoru Hirosaki University, Faculty of Science and Technology, Professor, 理工学部, 教授 (60196011)
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| Co-Investigator(Kenkyū-buntansha) |
OKAZAKI Isao Hirosaki University, Faculty of Science and Technology, Lecturer, 理工学部, 講師 (60332491)
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| Project Period (FY) |
2005 – 2006
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| Project Status |
Completed (Fiscal Year 2006)
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| Budget Amount *help |
¥2,500,000 (Direct Cost: ¥2,500,000)
Fiscal Year 2006: ¥1,100,000 (Direct Cost: ¥1,100,000)
Fiscal Year 2005: ¥1,400,000 (Direct Cost: ¥1,400,000)
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| Keywords | protein / atomic charge / molecular dynamics simulation / ab initio all electron calculation / localized orbital / quasi canonical orbital / force field parameter |
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| Research Abstract |
There are two important calculation methods for proteins, molecular dynamics (MD) simulation method and ab initio all electron calculation method. Our purpose was the improvement of the MD simulation method by combining ab initio all electron calculation method with it. The coworker is one of the authors of ab initio all electron calculation program (ProteinDF) and the head investigator is the author of a MD simulation program (COSMOS90). We improved the MD simulation method using precise atomic charges calculated by ProteinDF every thousands steps of MD. There are two methods calculating atomic charges based on (1)the Mulliken population analysis and (2)the electrostatic potentials (ESP) on the molecular surface. The ESP method is more reliable than the Mulliken method which depends on the basis sets used for expanding the wave functions. However, it is difficult to directly apply the ESP method to proteins, because we can not calculate the electrostatic potentials on the molecular surface for the buried amino acids of a protein. We overcame such difficulty by developing a new ESP method based on the localized orbital (LO). We checked that our method (so called ESPLO) give the precise atomic charges for a-helix and β-sheet. Next, we successfully performed MD simulations for a peptide consisting of 12 Gly residues in water. The ESPLO charges for the peptide were calculated every 1 ps using ProteinDF, where the water molecules around the peptide were represented by point charges. In principle, our methodology is applicable to a protein in water, but for the practical use we should accelerate the procedure making LO from MO.
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Report
(3 results)
Research Products
(5 results)
