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    Thanks many times for your guidance and help– I finally managed a solution based on your suggestions:

    1. I modified the __RMS_Energy__ constructor to read the option __~np~in::file::native_exclude_res~/np~__ and to convert it into __~np~std::list < core::Size > residue_selection_~/np~__ using __~np~protocols::evaluation::invert_exclude_residues~/np~__

    2. I added a few lines to __~np~RMS_Energy::finalize_total_energy~/np~__ to use __~np~residue_selection_~/np~__ as an additional argument to __~np~core::scoring::CA_rmsd~/np~__

    3. I created a weights patch file with “rms_energy = 1000”

    4. I added ~np~”-abinitio:stageX_patch {weights patch file}”~/np~ in my flags file to apply the RMS energy patch

    So far, it appears to be working nicely. Thanks again!