The vast majority of problems of this nature are caused by incorrectly set up ligand and/or protein input files. GOLD uses an all atom model, so the protein and ligand must have all hydrogen atoms added. In addition, each ligand and protein atom must be assigned an atom type. GOLD atom typing is based on SYBYL atom types; SYBYL bond types are also used. The correct assignment of atom and bond types is crucial for GOLD to function correctly.
Ligands will sometimes fail to dock if the binding site is too large or contains functionality that is not matched by equivalent functionality (donor, acceptor or hydrophobic) on the ligand. This is because GOLD requires at least three matches of complementary fitting points between protein and ligand before a binding pose can be scored. Where this is not achieved after a specified time the docking will fail with following error message:
Error message: Insufficient mapping points to define a 3D mapping
For further information about setting up your protein and/or ligand please refer to the GOLD user manual.