Tutorial for SDA 7
This tutorial is in examples/Tutorial_SDA7
It aims to present most of the functionalities of SDA 7 and to illustrate the preparation of the grids and of the effective charges, which are not always trivial.
It follows this structure :
- Installation and compilation
- Barnase-Barstar
- Step by step effective charges and grids calculations. Because of the force field nomenclature and default behaviour of some tools, we point out some potential problems, how to detect and how to correct them
- Protein-protein docking
- Association rate simulation
- Example of the usage of sda_energy and sda_koff
- Importin-Ran
- Illustrates the flexibility feature with the use of 3 conformations generated by Normal Mode Analysis of the Importin and a single conformation for Ran
- How to run a simulation in which one solute changes conformation during the trajectory
- How to run independent simulations where each one has a different conformation of the solute
- Multiple proteins simulation (SDAMM)
- 100 hydrophobins with a graphite surface
- The examples also illustrate the usage of the preparation and analysis tools provided with the distribution