GOLD fails to recognise the metal in my metal-containing enzyme
GOLD has parameters for a number of metals found in proteins but only the following metals are included: Mg, Zn, Mn, Fe, Ca, Co, Gd, Cu, Hg, Cd, Ni and V. If a metal not on this list is encountered by GOLD, then the following warning message is obtained:
Warning message: >> load_sybyl_molecule: read in unknown atom type## > > Setting atom ##### to type Du
A possible work-around is to re-type the metal atom in the protein input file to one of the included metal atom types listed above. The parameters for the chosen 'substitute metal' could then be altered (in the gold.params file) to values that are more appropriate for the 'real metal'.