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The simmechanics_to_urdf package will output a URDF file to standard out (if run using the xml option, which I assume you are). You should save this to a separate file and use that as your URDF file. You may want to run it like so...

rosrun simmechanics_to_urdf convert.py YOUR_XML.xml YOUR_CONFIG.yaml xml > YOUR_NEW_URDF.urdf

...and then use YOUR_NEW_URDF.urdf when trying to spawn in Gazebo.