Folding simulation of Trp-cage utilizing a new AMBER compatible force field with coupled main chain torsions

A newly developed AMBER compatible force field with coupled backbone torsion potential terms (AMBER03(2D)) is utilized in a folding simulation of a mini-protein Trp-cage. Through replica exchange and direct molecular dynamics (MD) simulations, a multi-step folding mechanism with a synergetic folding of the hydrophobic core (HPC) and the alpha-helix in the final stage is suggested. The native structure has the lowest free energy and the melting temperature predicted from the specific heat capacity C-v is only 12K higher than the experimental measurement. This study, together with our previous study, shows that AMBER03(2D) is an accurate force field that can be used for protein folding simulations.