I am performing docking claculations using RosettaLigand. I have two questions regarding RosettaLigand docking:
1. How does Rosetta ligand process the ligand conformers fed to dock a structure? I mean does it try all the ligand conformers sequentially in the input file or does it pick them randomly, if so on what criteria?
2. what is the basis for conformer being retained with model and produced as output: that is as a docked pose? is there any ratio (between the input ligand conformers and the ouput docked structures from each homology model in a docking run) that as to be followed depending on the conformers fed as input file to obtain the output docked poses, so that efficient sampling is done.