Abstract: In order to study the structure-function relationship in the protein which is incorporated with p-nitro-L-phenylalanine, the method of MD(Molecular Dynamics)simulation was established and successfully used in the analysis of protein which contains p-nitro-L-phenylalanine. The force field of CHARMM can only stimulate protein with natural amino acid in NAMD. Compared with phenylalanine, p-nitro-L-phenylalanine just has one more group of nitro. If the parameter of group of nitro was defined, the protein containing p-nitro-L-phenylalanine can be simulated. CGenFF-paramchem was used to calculate the energy and topological structure of p-nitro-L-phenylalanine′s new bonds(r), angles(θ), dihendrals(φ)and improper angle(ψ). And then the new defined parameter and topology information was input into the related parameter files and topology files in CHARMM. On the basis of correct parameter, NAMD can successfully simulate the modified BAFF(B lymphocyte stimulator)which contains p-nitro-L-phenylalanine. The changes in structure indicated that there might be new B cell epitopes. The temperature distribution of each frame in the process of dynamics stimulation was in accord with normal distribution, which proved the defined force field parameters was feasible. The RMSD of whole protein solution systemis 2. 5. Calculate each resides′ RMSF in BAFF, the RMSF of p-nitro-L-phenylalanine′s residue is 3. 7, which is obviously higher than that of the other residues in β-pleated sheet, and close to the loop rings, indicate that there might be variation in the area of p-nitro-L-phenylalanine residue and might produce new comformational epitopes. The results of MD stimulation will guide the immunogenicity experiments of p-nitro-L-phenylalanine modified proteins.