This example can be found in the directory examples/try-ben_modified_hd.
In this example case, hydrophobic forces are calculated with sasa values of 0 for atoms with a formal charge. These sasa values are read from a pdb file using the sasa_filename flag.The following table gives information about the different subfolders in the example directory:
| prepare_grids_and_ecm/ | Directory to generate the data files (pdbs, grids and effective charges) into the data_grid/ directory. Please run the run_ed_hd_ecm.sh to generate the necessary files to run the simulations. Make sure to set the correct path to the SDA installation. |
| data_grid/ | Data files (pdb and input files) needed for running the example. |
| try-ben_assoc_hits/ | Results of the example as it was run at HITS. |
| try-ben_assoc/ | Directory to run the try-ben_sdamd example. It uses the script_assoc.sh bash script. Make sure you have set the correct path for the SDA installation. |
| doc/ | Documentation of the Trypsin - Benzamidine simulation using customized sasa values for calculating hydrophobic forces. |
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 in the prepare_grids_and_ecm directory to generate the grids necessary to run this example. The grids will be copied to the data_grid directory.
Then go in the try-ben_assoc directory and run sda by executing the script_assoc.sh bash script.
You can check if the output files are similar to the ones generated at HITS: try-ben_assoc_hits/.
Note : you may need to adapt the shell scripts to your environment (location of APBS for instance)