@@ -29,7 +29,7 @@ Before you install the LAD Tools, you must first install the following software
2.**AutoDock4**: The docking engine used for simulations.
- Download: [AutoDock4 Official Page](http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page)
- Install the program and ensure it is in your system’s PATH.
- Install the program and ensure they are located in the workspace. See the folder structure below.
3.**OpenBabel**: Used for ligand file conversions (e.g., SDF to PDBQT).
- Download: [OpenBabel Official Page](https://openbabel.org/wiki/Main_Page)
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@@ -54,8 +54,11 @@ LAD Tools expects a specific folder structure to function properly:
│
├── /sdf_ligands # Place your SDF ligand files here (created by LightningScreen)
├── /ligand_pdbqt # Output directory for PDBQT files (created by LightningBabel)
├── /top_results # Directory where ranked results are places (created by LightningViewer)
└── /filtered_results # Directory for filtered results (created by LightningViewer)
├── /top_results # Directory where ranked results are placed (created by LightningViewer)
├── /filtered_results # Directory for filtered results (created by LightningViewer)
│
├── autodock4.exe # AutoDock4 executable for docking simulations
└── autogrid4.exe # AutoGrid4 executable for grid map generation
```
Beware that all ligand and protein files must be the workspace directory and not in subfolders. LightningAutoDock.py needs access to the files from the working directory. Also the protein needs to be named to "receptor.pdbqt".
