Rosetta Input/Output Paths (order essential)
path is first '/', './',or  '../' to next whitespace, must end with '/'
INPUT PATHS:
pdb1                            ./
pdb2                            ./
alternate data files            ./
fragments                       ./
structure dssp, ssa, dat, jones ./
sequence fasta, dat, jones      ./
constraints                     ./
starting structure              ./
data files                      ../../rosetta_database/
OUTPUT PATHS:
movie                           ./
pdb path                        ./output/
score                           ./output/
status                          ./
user                            ./
FRAGMENTS: (use '*****' in place of pdb name and chain)
2                               number of valid fragment files
3                               frag file 1 size
aa*****03_05.200_v1_3           name
9                               frag file 2 size
aa*****09_05.200_v1_3           name
