Search Of The Stable Conformations Of Lys-dipeptide And Lys-tripeptide By ABEEM??/MM Method

In this thesis,the basic polar lysine molecules with positive charge was used as the model molecule.The results are obtained from searching the stable conformations of lys-dipeptide and lys-tripeptide by ABEEM??/MM method,and that results are compared with the results by ab initio method.First of all,the potential energy surface of lys-dipeptide was obtained from B3LYP/6-311++G(d,p).After frequence calculated and structure optimized,all local minima were obtained.Then ABEEM??/MM method was used in the optimization of the stable structures from ab initio method.During the process,the paramethers of said chain dihedral angle were adjusted.When the consistency between ABEEM??/MM method and ab initio method was built,the same paramethers were applied to lys-tripeptide to justify their transfer.The whole results from force fields containing ABEEM??/MM,OPLS/AA,AMBER99 sb,CHARMM27 were compared with the results of ab initio method.ABEEM??/MM method is the only one method that can find out all the minima of ab initio method.After minimization,all the 19 types of lys-dipeptide stable structures and all the 46 types of lys-tripeptide stable structures were obtained from ABEEM??/MM.Based on value of backbone dihedral angles from ab initio method,the average absolute deviation(MAD)of lys-dipeptide and lys-tripeptide are 2.1° and 8.0° respectively.For lys-dipeptide,only 15 types,14 types and 15 types stable structures can be obtained from OPLS/AA,AMBER99 sb and CHARMM27.The MAD valves are 17.1°,16.1° and 10.8° respectively.For lys-tripeptide only 29 types,27 types and 17 types stable structures can be obtained from OPLS/AA,AMBER99 sb and CHARMM27.The MAD valves are 20.7°,24.6° and 17.4° respectively.From all above,ABEEM??/MM can find all stable structures with less wasting time,when compared with ab initio method.Bisides,the accuracy makes ti possible in studing larger range of biochemical systems.