FAQs
What is the naming convention for ligand output files?
Solution
The result of each docking attempt is written out as:
gold_soln_<ligand_name>_m#_n.mol2
where n is the solution number 1,2,3 ... and m# is the number of the ligand, i.e. m1 for the first ligand, m2 for the second, etc.
Please note that the file gold_soln_<ligand_name>_m1_1.mol2 is not necessarily the best GOLD prediction, it is only the solution found in the first docking attempt. However, as GOLD proceeds, symbolic links are created, such that ranked_<ligand_name>_m#_1.mol2 will always point to the current top-ranked solution, ranked_<ligand_name>_m#_2.mol2 will point to the second-best solution, and so on.