START
TARGET templates/src.SH3.pdb
FREE	templates/src.SH3.moved.pdb	# move the SH3 domain away from the bound peptide
FORCEFIELD ../../energy_function/forcefield
LIGAND	ligand_files/ala.ligand	#	1l	a
LIGAND	ligand_files/arg.ligand	#	2l	r
LIGAND	ligand_files/asn.ligand	#	3l	n
LIGAND	ligand_files/asp.ligand	#	4l	J
LIGAND	ligand_files/gln.ligand	#	5l	q
LIGAND	ligand_files/glu.ligand	#	6l	j
LIGAND	ligand_files/his.ligand	#	7l	o
LIGAND	ligand_files/ile.ligand	#	8l	i
LIGAND	ligand_files/leu.ligand	#	9l	l
LIGAND	ligand_files/lys.ligand	#	10l	B
LIGAND	ligand_files/met.ligand	#	11l	m
LIGAND	ligand_files/phe.ligand	#	12l	f
LIGAND	ligand_files/prt.ligand	#	13l	p	backbone and central pro
LIGAND	ligand_files/ser.ligand	#	14l	s
LIGAND	ligand_files/thr.ligand	#	15l	t
LIGAND	ligand_files/trp.ligand	#	16l	w
LIGAND	ligand_files/tyr.ligand	#	17l	b
LIGAND	ligand_files/val.ligand	#	18l	v
# MULTISTATE_JOBTYPE quench	optimized
# OUTPUT_PREFIX design_N_sub_peptide
MULTISTATE_JOBTYPE ga      optimized
OUTPUT_PREFIX design_N_sub_peptide.ga
OTHER_POSITIONS none
LOOKUP_TABLE_DIRECTORY  /whoa/usr/data/navin/lookup_tables/SH3.N_sub_peptide
VARIABLE_POSITIONS
1l	U.	# set all the default ligand positions to the U dummy residue
2l	U.
3l	U.
4l	U.
5l	U.
6l	U.
7l	U.
8l	U.
9l	U.
10l	U.
11l	U.
12l	U.
13l	U.
14l	U.
15l	U.
16l	U.
17l	U.
18l	U.	# follows are the actual N-sub peptide residues
1l	a,J,j,f,o,i,B,l,m,n,q,r,s,t,v,w,b.
2l	a,J,j,f,o,i,B,l,m,n,q,r,s,t,v,w,b.
3l	p.
4l	a,J,j,f,o,i,B,l,m,n,q,r,s,t,v,w,b.
5l	a,J,j,f,o,i,B,l,m,n,q,r,s,t,v,w,b.
89A	# the following are interface residues defined in 
90A	# ../../multistate/SH3_peptide/define_moving_residues/SH3.RALPPLPRY.complex_energy.out
91A	# these can change conformation
92A   
94A     
95A    
96A     
97A    
98A     
99A     
102A   
117A   
118A   
120A   
131A   
134A  
135A    
136A    
137A    
END