Calibration of force-field dependency in free energy landscapes of peptide conformations by quantum chemical calculations.
The free energy landscapes of peptide conformations were calibrated by ab initio quantum chemical calculations, after the enhanced conformational diversity search using the multicanonical molecular dynamics simulations. Three different potentials of mean force for an isolated dipeptide were individually obtained by the multicanonical molecular dynamics simulations using the conventional force fields, AMBER parm94, AMBER parm96, and CHARMm22. Each potential of mean force was then calibrated based upon the umbrella sampling algorithm from the adiabatic energy map that was calculated separately by the ab initio molecular orbital method, and all of the calibrated potentials of mean force coincided well. The calibration method was also applied to the simulations of a peptide dimer in explicit water models, and it was shown that the calibrated free energy landscapes did not depend on the force field used in the classical simulations, as far as the conformational space was sampled well. The current calibration method fuses the classical free energy calculation with the quantum chemical calculation, and it should generally make simulations for biomolecular systems much more reliable when combining with enhanced conformational sampling.
Ono
Satoshi
S
Mitsubishi Pharma Corporation, 1000 Kamoshida, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan.
Kuroda
Masataka
M
Higo
Junichi
J
Nakajima
Nobuyuki
N
Nakamura
Haruki
H
D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D011789:Quantum Theory; D014867:Water / Q000737:chemistry
D010455:Peptides; D014867:Water