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Agreed. I believe the "end-effector" group is used for some grasp-planning activities, and to display a "pretty" model at the desired end-effector location when using the planning tool, benchmarking tool, etc.

I talked some with Ioan (one of the primary moveIt developers) about this, and I think he's already implemented a cleaner solution for robots without a true "end-effector". It looks as if some fixes were implemented on March 18th, so you might keep an eye out for when these fixes are pushed out to the main debian-package repositories.

For now, the best solution is to create a "dummy" end-effector link in the robot's URDF:

<link name="dummy_eef"/>
<joint name="joint_6-eef" type="fixed">
  <parent link="link_6"/>
  <child link="dummy_eef"/>
</joint>