docking_scenario_names=qvina02_rigid_receptor1:smina_rigid_receptor1
This is the place where you place the config files relevant to the specific docking scenario
docking_scenario_programs=qvina02:smina_rigid
Respective binaries for the scenario mentioned above
docking_scenario_replicas=1:1
What does this mean?
Also, when the whole job is run, does it mean that the entire set of ligand library is docked using two programs? If so, will the results be stored separately?
Best regards,
Vishwa
Dear Vishwa,
Welcome to the VirtualFlow community 
The number of replicas per docking scenario means the number of time each docking program is run for each ligand. So it’s a replicate of the same computational docking experiment. But since docking contains probabilistic search algorithms, the results are not always the same. Thus the more often the same docking procedure is carried out, the more thoroughly the conformational space is explored, and the more likely it is that the best docking pose is found for a certain ligand. Alternatively, one can increase the exhaustiveness of a single docking run by increased the exhaustiveness parameter in the docking program configuration file.
The answer is yes to both questions.
How are the results of multiple replicas stored and reported? If I have 1000 ligands and set replicas to 2, will I have 2000 results? When I use the reporting tools will only the best docked pose from both replicas be reported? Thanks.