Aim. To parameterize a modified chained residue and use a newborn topology for molecular dynamics simulation. Methods. To deal with the problem, a series of ab initio and semi-empirical methods were combined. The RESP (Restrained ElectroStatic Potential) program, which fits molecular electrostatic potential (MEP) at molecular surfaces using an atom-centered point charge model. All parameters were quantum mechanically calculated and processed with R.E.D.III server. Results. The method of molecular dynamics has potential advantages, like its capability to explore large systems, and disadvantages, like not being feasible to run on fly without a preliminary prepared topologies for identification of each molecule. In an attempt to find a balance between both features speed and accuracy and apply the approach in a computational study, a functional mechanism of prolyl-tRNA synthetase from E. faecalis was investigated. In addition, a well validated protocol of topology preparation for non-canonical structure was developed. Conclusions. Computational approaches like molecular dynamics simulation and molecular docking had now become a strong in silico methods to study biological processes. The major benefits of this methods are expensiveness and speed. It also a strong competitor of quantum modeling approach. However, there is a need to include new structures that are not exist in the GROMACS library is associated with the growing use of different types of modified amino and nucleic acids (DNA derivatives and RNAs) both in fundamental studies in molecular biology, molecular biophysics, etc., and in applied research related to the search for new drugs. The obtained data well correlate with the experimental data.