| This paper apply self-compiled program automatic, precise and fast to scan the potential energy surface(PES) of val-dipeptide on the basic of ABEEMσπ/MM, whose results perfectly reproduced the PES by ab initio. Six types of stable conformations of val-dipeptide are obtained by the two methods. Meanwhile, AMBER 99 sb and OPLS/AA not only cannot scan the PES, but also only optimized three types on the basic of ab initio. This work has done a huge work of calibrating parameters. Taking the stable conformations of val-dipeptide as model molecules, the V1, V2, V3 and valence-state energy parameters of atoms have been calibrated to fit the geometry and energy of high level ab initio method. Then, the parameters were transfered to val-tripeptide systems. 34 types of stable conformations of val-tripeptide obtained by combinations of the backbone dihedral angles of the stable conformations of val-dipeptide. ABEEMσπ/MM can obtain all the 34 types of conformations of val-tripeptide as ab initio method, while OPLS/AA and AMBER 99 sb only can obtain 19 and 15 conformations, respectively. The MAD and RMSD of backbone dihedral angles of val-dipeptide by ABEEMσπ/MM, OPLS/AA and AMBER 99 sb are 5.3 °, 6.0 °, 6.9 °and 6.0 °, 6.6 °, 7.1 °, respectively. The MAD and RMSD of backbone dihedral angles of val-tripeptide by ABEEMσπ/MM, OPLS/AA and AMBER 99 sb are 5.2 °, 8.4 °, 9.0 °and 6.2 °, 9.0 °, 9.6 °, respectively. That means we can obtain the stable conformation of val-dipeptide and val-tripeptide by ABEEMσπ/MM. ABEEMσπ/MM also can calculate the total energy, the average absolute deviation of val-tripeptide is 1.65 kcal·mol-1 and the average relative deviation is 0.29×10-5, between the results from ABEEMσπ/MM and MP2/6-311++G(d,p) methods. The total energies of val-tripeptide are obtained by ABEEMσπ/MM faster 14250 times than that of MP2 calculations. That is the basic of calculating geometry and energy of other larger biological molecules. |
PDF Full Text Request