I'm trying to use the ddg_monomer application as described in the rosetta3.3 manual. It gives a command for preminimization of your input pdb structure using the application "minimize_with_cst". Trying this exact code with my pdb, or even with 2ci2.pdb found with the integration test, ends with "using -l option" as the last line of the output. Anyone else having similar problems or have a solution?
Also, the actual ddg_monomer application with 2ci2.pdb DOES work for me correctly.