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How do I define my active site?


The active site can be defined in one of several ways:

  • from an atom
  • from a point
  • from a reference ligand
  • from a file containing a list of atoms
  • from a file containing a list of residues

When using a list of residues to define the binding site the file must be in the following format:

> <Gold.Protein.ActiveResidues>
HIS69 ARG71 GLU72 ARG127 ASN144 ARG145 GLY155 ALA156 GLU163 THR164
HIS196 SER197 TYR198 SER199 LEU201 LEU203 ILE243 ILE244 ILE247 TYR248
GLN249 ALA250 GLY253 SER254 ILE255 THR268 GLU270 PHE279 ZN309

The list must be started by the line > <Gold.Protein.ActiveResidues> and must end with a blank line. Each of the residues must be separated by a space. GOLD writes additional information about the residues that it has read in the gold_protein.log.​