Interpolation schemes for peptide rearrangements

摘要

A variety of methods (in total seven) comprising different combinations of internal and Cartesiancoordinates are tested for interpolation and alignment in connection attempts for polypeptiderearrangements.We consider Cartesian coordinates, the internal coordinates used in CHARMM, andnatural internal coordinates, each of which has been interfaced to the OPTIM code and comparedwith the corresponding results for united-atom force fields. We show that aligning the methylenehydrogens to preserve the sign of a local dihedral angle, rather than minimizing a distance metric,provides significant improvements with respect to connection times and failures. We alsodemonstrate the superiority of natural coordinate methods in conjunction with internal alignment.Checking the potential energy of the interpolated structures can act as a criterion for the choice ofthe interpolation coordinate system, which reduces failures and connection times significantly.