Back to main GOLD page Each protein and ligand atom in a GOLD job must be assigned an atom type, which is used, for example, to determine whether the atom is capable of forming hydrogen bonds. GOLD atom typing is based on SYBYL atom types. SYBYL bond types are also used.
Correct assignment of atom and bond types is crucial. There are two ways in which they can be assigned. First, GOLD can assign them automatically from the atomic numbers and bond orders of the input structures. Secondly, the user can set them manually, via an input MOL2 file. Unless you are an expert GOLD user or are dealing with a very unusual ligand structure, you are recommended to use the automatic type-assigner. This requires that the "Set atom types" check buttons are switched on in the GOLD front end. However, even if you use this option, you still need to input the ligand and protein structures correctly, e.g. with correct bond orders and appropriate protonation states. It is not always obvious what "correct bond orders" means, especially for groups whose chemical structures can be drawn in more than one way, so please check out the following links carefully.
Notes on the Automatic Type-Assignment Software
Because correct atom typing is so important, any messages from the type checker are logged in both the log file and the error file. These errors will also be displayed in a separate window if GOLD is run through the front end.
Care should be taken when using the type-assignment software on protein input files. In particular, the software is likely to be unreliable if protein residues have been partially deleted, so that some atoms appear to have free valencies. This situation can be avoided by ensuring that all residues included in the input file are complete. If a PDB file is used to define the protein, then all residues should be complete.