Back to main GOLD page
As an alternative to SYBYL MOL2 file format, the ligand can be entered in MDL SD (standard drug) file format.
Please read the page on atom typing before specifying ligands in SD format.
SD format solutions can be viewed using the grommitt utility.
All hydrogens must be added to the ligand, including those necessary to resolve ambiguities in ionisation and tautomeric states. GOLD identifies the file format by the suffix of the input file. For SD input, the file should have the suffix .mol, .mdl or .sdf. The ligand should be in a low energy conformation.
After the ligand is read in, SYBYL atom types are automatically assigned, based on the bond environment of each atom (the special SYBYL bond types "ar" and "am" are also assigned). The page on general atom typing explains the bonding patterns that are required to identify particular hydrogen bonding groups and atom types.
Ligand solutions are written in the same file format as the input ligand file. For example, if the input ligand file is ligand.sdf, GOLD solutions will be written out in sd file format as ga_soln_ligand_1.sdf, ga_soln_ligand_2.sdf, etc.