For regular RosettaLigand ligand docking (using the XML scripts with the Transform and HighResDocker mover), the pocket in which you dock is typically specified by simply putting the ligand into roughly the area you want it to be in. (You start with the ligand in the pocket.) The RosettaLigand docking will then refine the position and orientation of the ligand.
If you have more complex requirements, the StartFrom mover is able to specify one or more locations. — But effectively what it does is automatically move the ligand from wherever it is to the location you specify. If you just have the one pocket, it’s often easier just to manually move the ligand to the pocket yourself, save that PDB, and then use that manipulated PDB as your starting structure for ligand docking.
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