Rosetta Input/Output Paths (order essential)
path is first '/', './',or  '../' to next whitespace, must end with /
INPUT PATHS:
pdb1	 ./
pdb2	 ./
pdb3	 ./
fragments	 ./
structure	 ./
sequence	 ./
constraints	 ./
starting structure	 ./
data files	DB_PATH
OUTPUT PATHS:
movie	 ./
pdb	 ./
score	 ./
status	 ./
user	 ./
FRAGMENTS:
2  number of fragment files
3  file 1 size
aa*****03_05.200_v1_3
9  file 2 size
aa*****09_05.200_v1_3