This page lists all the examples provided with the SDA 7 software release.
We advise you to run the barnase-barstar examples and the tutorial first. This is included in the distribution. You may find it easiest to run these examples on the webSDA web server first.
Additional information can be found in the README files or directly as comments in the shell script.
Please note that the examples have been prepared to demonstrate the functionality of SDA with rather short calculations. The parameters used in the examples do not necessarily match those used in published work. For the user's own applications, all parameter settings should be checked carefully and modified as necessary.
| 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 slab and 3 histidines peptide | au3his |
| Sample PMF calculation using DT-Grid compressed data structure | Gold slab and 3 histidines peptide | au3his-dtgrid |
| Compute the fraction of fluorescent particles in the analysis area in a trajectory obtained using Brownian dynamics. | Particles | rec-frap |
| Adsorption of Hen Egg-White Lysozyme to a Mica-Like Surface | Adsorption of many proteins to a charged surface | Lysozymes_mica |
| Adsorption of Hen Egg-White Lysozyme to a Mica-Like Surface (Gouy Chapman treatment) | Adsorption of many proteins to a charged surface (Gouy Chapman treatment) | Lysozymes_mica_gc |
| Tutorial | Included in the distribution. | |
| Convert to BrownDye/2 | Convert a SDA simulation setup to BrownDye (https://browndye.ucsd.edu/) from UCSD, US. | README |
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 |