Organizing your filesystem
INPHARMA calculations can be a complex business, and it will save you some headaches to properly organize your filesystem.
. |-- 01_prepare_structures | |-- 01_3DNE_LL1 | | |-- 01_build | | `-- 02_docking | | |-- _tmp_001 | | `-- pdbs_min | `-- 02_3DNE_M77 | `-- 01_build |-- 02_structures |-- 03_hlist |-- 04_asgn |-- 05_raw_data |-- 06_vols |-- 07_inpharma | |-- 01_LL1-M77 | `-- 02_LL2-M77
01_prepare_structures will contain all PDB files needed to run the INPHARMA calculation.
02_structures simply contains links to the 01 - directory.
Files for the INPHARMA run
03_hlist, 04_asgn, and 06_vols are all directories containing files for the INPHARMA calculation.
In the 07_inpharma directory we will perform all INPHARMA calculations. For each ligand-pair we are interested in we will make a seperate directory.