Feature: Making AutoDock Tools (ADT) Work for Your Research AutoDock Tools (ADT) is the essential graphical front-end for setting up and analyzing molecular docking simulations. As a part of the MGLTools suite, it provides a 3D interface to prepare receptors and ligands, define search grids, and visualize docking results. 1. Essential Downloads
conda install -c conda-forge mgltools or download tarball and run installer../mgltools_x86_64Linux2_1.5.7_installer.sh download autodock tools work
| Symptom | Root Cause | Fix |
| :--- | :--- | :--- |
| ADT window is blank/white | Missing or wrong Tcl/Tk version. | Install Tcl/Tk 8.5. On Windows, reinstall MGLTools. |
| "ImportError: No module named numpy" | ADT's internal Python cannot find math libs. | Install Miniconda, create a Python 2.7 env, and symlink the numpy folder. |
| "ERROR: Can't find autodock4" | Paths not set. | Manually set paths in ADT's Preferences. |
| "Segmentation fault" on Linux | OpenGL library conflict. | Run export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6 before launching ADT. |
| PDBQT files have zero atoms | The input PDB has non-standard residues. | Clean your PDB file using a tool like pdb4amber first. | Feature: Making AutoDock Tools (ADT) Work for Your
C, OA, NA).AutoDock Tools (ADT) is a Python-based graphical front-end for AutoDock 4 and AutoDock Vina. Its primary job is to prepare molecular files for docking and analyze the results. Specifically, ADT allows you to: MGLTools:
| Problem | Likely Solution |
| :--- | :--- |
| ADT opens but is blank/white | Update your graphics drivers. On Linux, disable 3D acceleration in the VM. |
| "Can't find python" error | Reinstall and ensure the PATH is set. ADT bundles its own Python. |
| Mac: "X11 connection rejected" | Start XQuartz first. Then run export DISPLAY=:0 in terminal before launching ADT. |
| Windows: Missing DLL errors | Install Microsoft Visual C++ Redistributables (2015-2022). |