Combining Docking, Molecular Dynamics Simulation, and Free Energy Calculation to Improve the Accuracy of Virtual Screening of Drug Candidates Against HIV Integrase

In order to be better prepared for the research, our group did Amber tutorial B0 as a start. Amber is the abbreviation for “Assisted Model Building and Energy Refinement.” It is a set of force fields that describe the potential energy function and parameters of the interaction of biomolecules. It also refers to a package of molecular simulation programs which includes source code and demos.

Our group worked on a computer with AmberTools v15, VMD, and xmgrace installed. The AMBER tutorial B0 asks us to run a molecular dynamics simulation and analyze the results. The steps include preparing topology and coordinate files, loading a protein and nucleic acid force field, building alanine dipeptide, solvating alanine dipeptide, minimizing input, running Amber MD sander, running minimization, running heating MD, and running production MD. Completing Amber tutorial enabled our group to become familiar with Linux and the Amber software.