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Directory description

This example can be found in the directory examples/bnbs.

This is the main page for all barnase-barstar examples, the links below will redirect you to the specific page.

The following table gives information about what the respective examples demonstrate :

prepare_grids_and_ecm/ Directory to generate the data files (pdbs, grids and effective charges) into the data_grid/ directory
data_grid/ Data files (pdb and input files) needed for running the barnase and barstar examples
bnbs_assoc_hits/ Results of the examples for barnase-barstar association rates run at HITS (more details)
bnbs_assoc/ Directory to run the barnase-barstar association rate simulations
bnbs_docking_hits/ Results of the example for barnase-barstar docking run at HITS (more details)
bnbs_docking/ Directory to run barnase and barstar docking simulation
bnbs_koff/ Input and output files to compute barnase-barstar residence time (more details)
bnbs_energy/ Input and output files to compute the energy of complexes with a different set of interactions (more details)
doc/ This documentation
unit-test/ For developers, regression tests for many different combinations of interactions. The grids need be generated first

Running examples

Assure you have compiled all the executables and tools in sda_flex/bin/ first or refer to the compilation section.

Run first the script run_ed_hd_ecm.sh from prepare_grids_and_ecm to generate the grids necessary to run all the barnase-barstar examples.

Then go in one of the directories containing a script or an input file and execute either :

./script_assoc.sh

or if a script is not provided :

../../../bin/sda_flex sda_input.in > sda_out

You can check if the output files are similar to the ones generated at HITS: bnbs_assoc_hits/ and bnbs_docking_hits/ or to the provided output files (bnbs_koff/ and bnbs_energy/).

Note : you may need to adapt the shell scripts to your environment (location of APBS for instance)

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