I am trying to make iterations between KIC and fbb. fbb design accepts multiple inputs through -l option. I cant find a similar option for KIC. I can only input one pdb at a time using the option -loops:input_pdb. I tried putting multiple pdbs using -loops:input_pdb but it gave me: ERROR: Multiple values specified for option -loops:input_pdb.
Loop modeling does not support multiple input files the way fixbb does because it does not obey the Rosetta standard -s/-l inputs. One possible reason is that loop model requires fragment and loop definition files, which are unlikely to be compatible between different input structures; this forces separate runs for separate inputs. Another possible reason is that it has yet to annoy anybody enough that they’ve bothered fixing it.
The easy fix is to organize your separate runs by stitching them together with a shell script.