A Program to Repack Protein Side-chains for Protein Docking Refinement Procedures
Copyright (c) 2014, Structural Bioinformatics Laboratory, Boston University
Author: Mohammad Moghadasi (mohamad@bu.edu) 

Requirements:

I. Install libmol library
	instructions at https://github.com/StructuralBioinformaticsLab/libmol

II. Obtain Charmm parameters
	instructions:
		1. curl http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c36_aug14.tgz | tar xz
		2. cp toppar/toph19.inp prms/pdbamino_new.rtf
		3. cat toppar/param19.inp toppar/ace/acepar19.inp > prms/parm_new.prm

III. build the program
	instructions:
		1. make

IV. run the program
	instructions:
		1. do "./run.sh"
		2. find the output file in "1dfj/" as 1dfj_mwis_repacked.pdb


Supplement - Example of protein preparation:
You will need:
	(1) https://github.com/Acpharis/protein_prep
	(2) https://github.com/Acpharis/create_psf
	(3) https://github.com/Acpharis/pdb_utils
	(4) OpenBabel ( https://github.com/openbabel/openbabel )

Step 1: Prepare the PDB
	protein_prep/prepare.py 1dfj.pdb
	This creates 1dfj_pnon.pdb

Step 2: Create the PSF
	create_psf/create_psf_dihe 1dfj_pnon.pdb prms/pdbamino_new.rtf 1dfj_pnon.psf
	This creates 1dfj_pnon.psf

Step 3: Extract the ligand (chain I of 1dfj)
	pdb_utils/extract_chain 1dfj_pnon.pdb I > 1dfj_pnon_l.pdb

Step 4: Create mol2 file
	obabel 1dfj_pnon.pdb -O 1dfj_pnon.mol2

Now you can run the program
	./main 1dfj_pnon.pdb 1dfj_pnon.psf 1dfj_pnon.mol2 1dfj_pnon_l.pdb prms/atoms.0.0.6.prm.ms.3cap+0.5ace.Hr0rec prms/parm_new.prm prms/pdbamino_new.rtf prms/rotamer_lib.txt 1dfj_repacked.pdb