You need to align the gripper, so that the axis of grip (line between the two gripper fingers) lines up with the axis of the tool, and the main plane of the gripper is horizontal (in the same plane as the tool.) Then you can lower the gripper, and make the fingers tighten. You need either force sensors, or very accurate measurements, or grippers designed for significant slop, to avoid locking up the actuators of the gripper fingers when they stop against the tool.