Rosetta Input/Output Paths (order essential)
path is first '/', './',or  '../' to next whitespace, must end with '/'
INPUT PATHS:
Native structure                ./
Unbound structure               ./
alternate data files            /home/aroop/simcode/rosetta_database/
fragments                       ./
structure dssp,ssa (dat,jones)  ./
sequence fasta,dat,jones        ./
constraints                     ./
starting structure              ./
data files                      /home/aroop/simcode/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_05.200_v1_3                               name
9                                      frag file 2 size
aa*****09_05.200_v1_3                               name
------------------------------------------------------------------------
Information for new users:

Edit the lead part of the two database paths so that they are consistent
with the structure of your filesystem and your user name.

Note that all paths must end with '/'.  Otherwise paths.txt will not work.
"alternate data files" and "data files" should point to the location of the
 rosetta_database module.
Pay careful attention to the difference between native structure, starting 
structure, unbound structure, etc.  These terms are defined in the RosettaDock
tutorial.

The reference directory (./) refers to the directory in which Rosetta 
outputs pdb files (rrun.sh should create this directory).  Thus, the 
directory from which you launch rrun.sh is '../' and not './'
-------------------------------------------------------------------------
CVS information:
$Revision: 1.2 $
$Date: 2005/03/02 22:23:05 $
$Author: mdaily $
-------------------------------------------------------------------------
