The SDA program itself can be executed by typing:

sda_flex/bin/sda_flex

If no input file is provided, a short help is printed (this is also the case for all the tools compiled in bin/)

To run a simulation properly though, you need to provide an input file:

sda_flex/bin/sda_flex input-file > output-file

A full description of the input file format is provided here, the output files are described here, and the tools are described on this page.

The easiest way to begin to use SDA is to:

• Run webSDA to become familiar with the workflow.
• Run one of the many examples provided in sda_flex/examples/. A summary can be found on this page
• Follow the detailed, but not completely updated tutorial in sda_flex/examples/Tutorial_SDA7/

To run SDA, you have to prepare:

1. PDB files of the solutes;
2. files with reaction atoms, 1 file for each pair of solutes; You next need to decide which types of interactions to compute. For a description of the different terms, see the Appendix in Martinez et al,

If electrostatic interactions are to be taken into account, then you must provide:

3. files with the electrostatic potential in UHBD format;
4. files containing effective charges calculated with ECM

If the forces due to desolvation are to be taken into account, then you need also:

5. electrostatic and the non-polar desolvation grids for each solute (see the description of the input file for details)

If the Lennard-Jones or soft-core repulsion interactions are to be taken into account, prepare:

6. Lennard-Jones grid(s) of solutes and the probe site identifier for each atom of the other solute (see the description of the input file for details)

If protein adsorption on a solid surface is to be simulated, then:

• the solid surface should be represented as a slab of several atomic layers in PDB format
• the solid surface can be modeled as a zero-potential surface or as a set of charged atoms. In the latter case, an electrostatic grid for the surface and a file that defines surface charges are needed (see the description of the input file for details)

If DT-Grid structure for efficient data compression is to be used, then you need:

• a DT-Grid format file converted from UHBD format using UHBD2dtgrid tool.
• to rename the file as pdb_filename.excl.ascii/bin.grd and to store in the same directory with the input pdb file, if this is an excluded volume type grid!

These pdb and grid files can be located anywhere as long as the relative or absolute paths to these files are given correctly in the input file. Output files will be written in the directory where SDA is executed. The main calculation results are written to standard output which can be redirected to a file as in the above execution example.

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