Our research group has done a few AMBER tutorials during the Fall 2018 semester, and we will meet twice a week during winter break to continue the research. These tutorials provided us information about how to use the AMBER software and how to run simulations efficiently. Tutorial B1 is one of them and it prepares our research group well for the future steps.
The goal of AMBER tutorial B1 is to simulate a DNA polyA-polyT Decamer. First we made sure that the required files prmtop, rst7, mdin are set up. Then we performed basic RMSd analysis and visualized the results with VMD. After that we used the Born implicit solvent model to run MD simulation for the DNA model. Last we used TIP3P explicit water to run production simulation.
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.