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)|
|unit-test/||For developers, regression tests for many different combinations of interactions. The grids need be generated first|
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 :
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)