Improvement of the backbone-torsion-energy term in the force field for protein systems by the double Fourier series expansion

Abstract

We have previously proposed a force-field refinement method. This method consists of minimising the sum of the square of the force acting on each atom in the proteins with the structures from the Protein Data Bank. In addition, we also proposed a new backbone-torsion-energy term, which is represented by a double Fourier series in two variables, the backbone dihedral angles and . In this paper, we apply our optimisation method and backbone-torsion-energy term to AMBER ff94 (ff96) force field for molecular simulation of protein systems. The results imply that the new force-field parameters give structures of two peptides more consistent with the experimental implications for secondary-structure-forming tendencies than the original force field.