Rosetta Input/Output Paths (order essential)
path is first '/', './',or  '../' to next whitespace, must end with '/'
INPUT PATHS:
pdb1	                        ../1d3z/ 
pdb2                            ../
data files (alternate)          ../../rosetta_database/ 
fragments                       ../1d3z/
structure-dssp,ssa (dat,jones)  ../1d3z/ 
sequences- fasta,dat,jones      ../1d3z/ 
constraints                     ../1d3z/
starting structure              ../1d3z/
data files                      ../../../rosetta_database/
OUTPUT PATHS:
movie                           ./
pdb path                        ./
score                           ./
status                          ./
user                            ./
FRAGMENTS: (use '*****' in place of pdb name and chain)
2                                      number of valid fragment files
3                                      frag file 1 size
aa*****03_06.200_new_d                               name
9                                      frag file 2 size
aa*****09_06.200_new_d                               name
