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.
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