Relative Energies of Proteins and Water Clusters Predicted with the Generalized Energy-Based Fragmentation Approach

Abstract

A generalized energy-based fragmentation (GEBF) approach we developed recently [57] is applied to investigate the relative energies of many conformers of two proteins (PDB id: 2ETI and 1CMR) and one water cluster (H2O)20. The GEBF results are compared with those from conventional quantum chemistry methods, empirical molecular mechanics (MM), and semi-empirical quantum mechanical methods (AM1, PM3). Our computational results show that for all three systems, not only the total energies but also the relative stabilities of their different conformers predicted by the GEBF approach are fairly consistent with those from the corresponding conventional quantum chemistry method, while the widely used MM and semi-empirical QM methods give poor descriptions for the relative energies of different conformers.