Informational and File Sharing Server
Modeling of Macromolecular Systems
Tutorials
Tutorial 1: Molecular dynamics simulation of protein
This tutorial illustrates how
to perform protein simulation in Amber 10 / AmberTools 1.2 package. We will prepare and solvate start system, run energy
minimization and molecular dynamics.
Tutorial 2: Including ligands in protein simulation
This tutorial illustrates how to include small molecules such as substrate or cofactor in you simulation
by Amber 10 / AmberTools 1.2 package. It's also will be demonstrated how to develop parameters for a new molecule
by AmberTools 1.2, PC Gamess/Firefly and R.E.D.-III.2.
Tutorial 3: Steered molecular dynamics
This tutorial illustrates how
to perform steered dynamics in Amber 10.
Tutorial 4: Using VMD
This tutorial illustrates how
to use VMD to vizualise your molecules and trajectories.
Links: