Peptide free energy landscapes calibrated by molecular orbital calculations.
Free energy landscapes of peptide conformations werecalibrated by ab initiomolecular orbital calculations, after enhancedconformational sampling using the multicanonical molecular dynamicssimulations. Three different potentials of mean force for an isolateddipeptide were individually obtained using the conventional force fields,AMBER parm94, AMBER parm96, and CHARMm22. Each potential ofmean force was calibrated based on the umbrella sampling algorithm fromthe adiabatic energy map that was calculated separately by the abinitiomolecular orbital method. All the calibrated potentials of mean forcecoincided well. The calibration was applied to a peptide in explicit water,and the calibrated free energy landscapes did not depend on the force fieldused in conformational sampling, as far as the conformational space waswell sampled.
Mitsubishi Pharma Corp., 1000 Kamoshida, Aoba-ku, Yokohama, Kanagawa, 227-8502 Japan.
S
S
Ono
M
M
Kuroda
J
J
Higo
N
N
Kamiya
N
N
Nakajima
H
H
Nakamura
force field; multicanonical molecular dynamics; peptide conformations; potential of mean force; quantum chemical calculation; structural ensemble