Before diving into the process, it is important to understand why this tool remains a staple in scientific literature decades after its initial conception.

: Run via terminal using java -jar /path/to/LigPlus.jar .

: Visualizes interactions across protein-protein or domain-domain interfaces. Automation

Your PDB file must adhere to standard PDB formatting. Use tools like PDBfixer (available with Ligplot+) or manually check that HETATM records for the ligand are present and connected.