Application Of ABEEM/MM Force Field For Protein Model To Study Conformational Properties Of Dipeptide

Peptide molecules play very important roles during a number of biochemical processes.The conformers have been the subject of our investigations in gas state and solution chemistry. NMR many experiment techniques can offer the correlative information for us, but that doesn't satisfy our requirements. Simulation of computational chemistry has been an important tool, while simulation results depend on the quality of the molecular force field. To date, there has been a major problem in the widely used protein force fields, in which modeling of the electrostatic interaction plays an important role in describing the dynamical and structural properties of a system, and all electrostatic polarizations and charge-transfer effects are neglected explicitly. The use of atom-centered charges (as opposed to be a more accurately achieved by explicitly representing bond and lone pair) is another challenge for traditional fixed charge force fields. Hence, there are many scientists who are working in exploring and developing new methods that can effectively and reasonably compute the electrostatic polarizations of molecules and systems according to the changes of the environment.Based on the electronegativity equalization principle ,Yang et al. have delivered and developed the Atom-bond Electronegativity Equalization method (ABEEM) to computed the charge distributions of the large organic and biological molecules with accuracy. The method has been received considerable interest in recent years. In the ABEEM model, the partial charges are treated explicitly including atom, bond and lone-pair regions and responsible to the ambient environments. According to the above requirements of the polarizable force field, the ABEEM/MM fluctuating charge force field for proteins has been constructed on the basis of the combination of the ABEEM method and molecular mechanics. In this paper, the...