Polarizable force field for protein with charge response kernel

Miho Isegawa, Shigeki Kato

    Research output: Contribution to journalArticlepeer-review

    11 Citations (Scopus)

    Abstract

    We present a molecular mechanical force field for polypeptides and proteins involving the electronic polarization effect described with the charge response kernel. All of the electrostatic parameters for 20 amino acids are obtained by ab initio electronic structure calculations and combined with the AMBER99 force field. The refittings of dihedral angle parameters in the torsional potentials are performed so as to reproduce the ab initio optimized geometries and relative energies for the conformers of dipeptides. The present force field is applied to molecular dynamics simulation calculations of the extended alanine tetra and cyclic pentapeptides in aqueous solution. The infrared spectra are calculated in order to analyze the charge polarization effect on the spectral profiles.

    Original languageEnglish
    Pages (from-to)2809-2821
    Number of pages13
    JournalJournal of Chemical Theory and Computation
    Volume5
    Issue number10
    DOIs
    Publication statusPublished - Oct 2009

    All Science Journal Classification (ASJC) codes

    • Computer Science Applications
    • Physical and Theoretical Chemistry

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