Rosetta Input/Output Paths (order essential)
path is first '/', './',or  '../' to next whitespace, must end with '/'
INPUT PATHS:
pdb1	                        ../2ptl/ 
pdb2                            ../
data files (alternate)          ../rosetta_database/
fragments                       ../2ptl/
structure-dssp,ssa (dat,jones)  ../2ptl/ 
sequences- fasta,dat,jones      ../2ptl/ 
constraints                     ../2ptl/
starting structure              ../2ptl/
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
*****03.200_new_d                               name
9                                      frag file 2 size
*****09.200_new_d                               name