List of examples
This page lists all the examples provided with the SDA 7 software release.
We strongly advise you to make at least once the barnase-barstar examples and the tutorial.
Additional information can be found in the README
files or directly as comments in the shell script.
Calculation type | Solutes | Example name and link |
---|---|---|
Bimolecular Association Rate Constant | barnase and barstar | bnbs-assoc |
Rigid/body docking | barnase and barstar | bnbs-docking |
Bimolecular Dissociation Rate Contstant | barnase and barstar | bnbs-koff |
Intermolecular energy | barnase and barstar | bnbs-energy |
Electron transfer rate | Cytochrome f and plastocyanin | cytf pc |
Protein-surface binding using the ProMetCS force field | Gold slab and barnase | aubs |
Diffusion of many rigid protein molecules | 128 lysozyme molecules | Lysozymes_128 |
Diffusion of many flexible protein molecules | 128 lysozyme molecules (configurations for pHs 3, 6 and 9) | Lysozymes_128_flex |
Diffusion of many proteins close to a surface | Graphite surface and hydrophobin molecules | HFBI-graphite |
PMF calculation between a tripeptide and a surface | Gold slad and 3 histidines peptide | au3his |
Tutorial | Tutorial |
Structure of the examples diectories
Each example directory has similar sub-directories, containing the input data, output data and scripts.
data_grid/ |
Data files: PDB files, accessibility files (*.access ) and grids (electrostatics: *.ep.grd , electrostatic desolvation: *.ed.grd , non-polar desolvation: *.hd.grd , and repulsion: *.lj.grd ) |
prepare_grids_and_ecm/ |
Scripts necessary to generate the grids (these can be used as a template for different setups) |
[simulation_type]/ |
The main directory for running each simulation (input and output files) |
[simulation_type]_hits/ |
Directory where we run simulations at home (HITS), you can compare output files with your own run in [simulation_type] |
[simulation_type]/unit_test |
For developers, directory to run regression tests |
[simulation_type]/generate_init_pos/ |
Scripts and outputs to generate the initial positions for SDAMM-type simulations |
[simulation_type]/analysis/ |
Scripts containing exemplary usage of SDA7 tools for analysis of SDAMM-type simulations |