# This reads in the template pdb file and thus allows us to use the @nonhydrogens
# special group later in the input
MOLINFO STRUCTURE=beta-hairpin.pdb MOLTYPE=protein

# The following commands compute all the Ramachandran angles of the protein for you
r2-phi: TORSION ATOMS=@phi-2
r2-psi: TORSION ATOMS=@psi-2
r3-phi: TORSION ATOMS=@phi-3
r3-psi: TORSION ATOMS=@psi-3
r4-phi: TORSION ATOMS=@phi-4
r4-psi: TORSION ATOMS=@psi-4
r5-phi: TORSION ATOMS=@phi-5 
r5-psi: TORSION ATOMS=@psi-5 
r6-phi: TORSION ATOMS=@phi-6 
r6-psi: TORSION ATOMS=@psi-6 
r7-phi: TORSION ATOMS=@phi-7 
r7-psi: TORSION ATOMS=@psi-7 
r8-phi: TORSION ATOMS=@phi-8 
r8-psi: TORSION ATOMS=@psi-8 
r9-phi: TORSION ATOMS=@phi-9 
r9-psi: TORSION ATOMS=@psi-9 
r10-phi: TORSION ATOMS=@phi-10  
r10-psi: TORSION ATOMS=@psi-10  
r11-phi: TORSION ATOMS=@phi-11  
r11-psi: TORSION ATOMS=@psi-11  
r12-phi: TORSION ATOMS=@phi-12  
r12-psi: TORSION ATOMS=@psi-12  
r13-phi: TORSION ATOMS=@phi-13  
r13-psi: TORSION ATOMS=@psi-13  
r14-phi: TORSION ATOMS=@phi-14  
r14-psi: TORSION ATOMS=@psi-14  
r15-phi: TORSION ATOMS=@phi-15  
r15-psi: TORSION ATOMS=@psi-15  
r16-phi: TORSION ATOMS=@phi-16  
r16-psi: TORSION ATOMS=@psi-16  

# This command stores all the Ramachandran angles that were computed
cc: COLLECT_FRAMES ARG=r2-phi,r2-psi,r3-phi,r3-psi,r4-phi,r4-psi,r5-phi,r5-psi,r6-phi,r6-psi,r7-phi,r7-psi,r8-phi,r8-psi,r9-phi,r9-psi,r10-phi,r10-psi,r11-phi,r11-psi,r12-phi,r12-psi,r13-phi,r13-psi,r14-phi,r14-psi,r15-phi,r15-psi,r16-phi,r16-psi

# This command outputs all the Ramachandran angles that were stored to a file called angles_data
OUTPUT_ANALYSIS_DATA_TO_COLVAR USE_OUTPUT_DATA_FROM=cc ARG=cc.* FILE=angles_data

