Is it possible for me to use the .prm and .rtf files from my original system, which already contain the CMAP stub and the dihedral definition, and load them manually during Step 1 of the Membrane Builder instead of generating new files? My hope is that CHARMM will automatically include the cross-terms in the Step5_assembly.psf file and use the correct atom typing. I would just cut that block and paste it into the psf for the original system.