Organizing your filesystem

INPHARMA calculations can be a complex business, and it will save you some headaches to properly organize your filesystem.

Overview

.
|-- 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

Prepare structures

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.

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.

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