Sorry to bother you with this, I should have figured it out before posting to the forum. After knowing what the problem is the manual make sense, but at first I figured that it would just print out things specific to that system and didn’t know that it would fail completely. I would suggest just putting stronger language such as saying that this must be removed or it won’t work for any system but the example.
thanks for the help
> I am trying to model the ends of a protein structure that extend beyond what I have in the PDB file. I tried using the FloppyTails protocol but that seemed to only work for really long tails (> 30aa) and gave me a segmentation fault when I tried to make them shorter (3-10 aa). Does anyone know of a way to use the loop prediction or modify the floopy tails protocol to get this to work?