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So it seems like this problem was addressed here but doesn't seem to be working for me. As a workaround, I added initial joint positions in the launch file when spawning the robot in Gazebo:

<node name="spawn_urdf" pkg="gazebo_ros" type="spawn_model" args="-param robot_description -urdf -model panda -J panda_joint4 -1.571 -J panda_joint6 1.571 -J panda_joint7 0.785 -unpause"/>

Note, that Gazebo needs to be started paused for the initial joint positions to be set correctly as I believe this is a bug in Gazebo.