1. Download antibody sets

2. Change ~/antibody/scripts/rampaths.txt to set the paths to match your directory structure

3. Copy the following files to directory where simulation will be run:
	 a. ~/antibody/scripts/rampaths.txt
	 b. ~/antibody/scripts/utilities.txt

4. Have the following files ready for input in the simulation directory:
	 a. query_l.fasta: sequence of light chain
	 b. query_h.fasta: sequence of heavy chain
	 Note: The fasta files should conform to the following format:
	       i.  The header line with > should not be there
	       ii. There should not be any hyphens for breaks
	       iii.There should not be any newline charchter - all on one line		 

5. Make sure that Profit is installed on your system and it is set up
	 such that it can be called from any subfolder by typing "profit".

6. Change the paths.txt in  ~/antibody/scripts/paths.txt
	 such that in all cases it points to your local copy of the rosetta_database directory

7. Change the hardcoded paths in the file ~/antibody/scripts/ram_blankcdrs.pl
   They should point to two files located in ~/antibody/scripts/. Make sure that the full 
   absolute paths (non-relative) are provided. For some strange reason incorporating rampaths.txt 
   does not work here, more details are provided in ram_blankcdrs.pl

8. Also ensure that you have the most updated version of the rosetta_database directory

9. Change paths for sam/jufo/blosum etc in the following file: ~antibody/scripts/make_rosetta_fragments.pl

10.In the folder in which simulations will be run,which already contains:
   i.   rampaths.txt
   ii.  utilities.txt
   iii. query_l.fasta
   iv.  quary_l.fasta
	
   Launch the following command:
   perl -P ~/antibody/scripts/ram_buildloop_wrapper4.pl pdb1xyz_chothia.pdb bit ram ram 1 1 1 1 1 0 0 1 1 0 0 0 0 FR02 2 1 3 2000 2000 3 0 query_l.fasta query_h.fasta

11.The simulations folder will have a new directory named "build". Some of the
   important files in the directory are:
   i.   FR02.pdb: The framework region with the non-H3 CDRs grafted in
   ii.  H3_CTERM: Fragment files for the CDR H3 base region
   iii. aaFR02_03_05.200_v1_3: 3-mer fragment file for the H3 loop region with antibody fragments appended.
   iv.  aaFR02_09_05.200_v1_3: 9-mer standard rosetta fragment
   v.   lfr.pdb: light chain template from which light chain of FR02.pdb has been obtained
   vi.  hfr.pdb: heavy chain template from which heavy chain of FR02.pdb has been obtained
   vii. 1xyz_build_loops.con: The condor script file containing headers. This is used for launching jobs on the 
	cluster using the command: "condor_submit 1xyz_build_loops.con"
   viii.1xyz_build_loops.bash: This is called by the .con file (above) and contains the actual rosetta command 
        line needed for launching a job with 2000 decoys.

Rosetta command line example:
rosetta.gcc aa FR02 _  -s FR02 -nstruct 1 -antibody_modeler -quiet -h3
-H3_filter -ex1aro -ex2aro_only -find_disulf -norepack_disulf
-norepack_antibody -unboundrot -use_pdb_numbering -ccd_closure -loop_frags
-build_loop -compute_hbond -max_frags 350 -relax_cdrs -freeze_h3 -flank_relax
2


Reference:
Manuscript in preparation: "High-resolution homology modeling of
antibody Fv regions and application to antibody-antigen docking"
Arvind Sivasubramanian, Aroop Sircar, Sidhartha Chaudhury & Jeffrey
J. Gray, 2008

