Application of the fragment molecular orbital method for determination of atomic charges on polypeptides. II. Towards an improvement of force fields used for classical molecular dynamics simulations

Yoshio Okiyama, Hirofumi Watanabe, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Takeshi Ishikawa, Kuniyoshi Ebina, Shigenori Tanaka

Research output: Contribution to journalArticlepeer-review

24 Citations (Scopus)

Abstract

The restrained electrostatic potential (RESP) fitting method with a harmonic restraint toward target values is applied to determination of atomic charges on polypeptides on the basis of the fragment molecular orbital method. The present RESP charges are determined to be confined around the targeted Amber 94 charges with high-fitting quality, including structural specificity; an optimal value of restraint weight makes the fitted charges reliable and stable. We employ the optimally-weighted RESP charges for an improvement of force fields in molecular dynamics simulation and show that the charges keep good reproducibility of the electrostatic properties during the simulation.

Original languageEnglish
Pages (from-to)417-423
Number of pages7
JournalChemical Physics Letters
Volume467
Issue number4-6
DOIs
Publication statusPublished - 2009 Jan 5
Externally publishedYes

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

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