Optimisation of OPLS–UA force-field parameters for protein systems using protein data bank

We have previously proposed a method for refining force-field parameters of protein systems, which consists of minimising the summation of the square of the force acting on each atom in the proteins with the structures from the protein data bank (PDB). The results showed that the modified force-field parameters for all-atom model gave structures more consistent with the experimental implications than the original force fields. In this work, we applied this method and a new method to the OPLS–UA force field. In the new method, we perform a minimisation of the average of the root-mean-square deviation of various protein structures from the native structure. We selected some torsion-energy parameters for this optimisation, and 100 molecules from the PDB were used. The results imply that the new force-field parameters gave structures of two peptides more consistent with the experimental implications for the secondary structure-forming tendencies than the original OPLS–UA force field.