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

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