# Load settings
source 1fx7_ms2_settings.bcl

# Create non-standard residue library
createStdGroup NAME
copyStdResidue aminoAcids94/MET NAME/MEF
copyStdResidue aminoAcids94/CYM NAME/CYF
copyStdResidue aminoAcids94/GLU NAME/GLT
copyStdResidue aminoAcids94/HID NAME/HIT
copyStdResidue aminoAcids94/MOH NAME/OH1
copyStdResidue metals/.FE NAME/FE2

# Create new atom types
copyAtomType parm99/S NAME/SA    # from xleap we identify the atom type for NE2 in HID. It is called NB and thus that is copied. Same is done for all other atoms bonded to the metal
copyAtomType parm99/SH NAME/SB
copyAtomType parm99/O NAME/OC
copyAtomType parm99/O2 NAME/OD
copyAtomType parm99/NB NAME/NL

setAtomType NAME/MEF/.SD. NAME/SA  #assign each atom there respective atom type
setAtomType NAME/CYF/.SG. NAME/SB
setAtomType NAME/CYF/.O.. NAME/OC
setAtomType NAME/GLT/.OE1 NAME/OD
setAtomType NAME/HIT/.NE2 NAME/NL

# write standard library
writeLib NAME NAME.xml

# Open PDB file
readPdb NAME NAME_fixed.pdb

# Assign S-S bonds
assignDisulfideBonds

# Atom type
atomType

# Assign bonds, angles, and torsions
assignConnectivity

# Add hydrogens
addHs /NAME/

#################### CLUSTER ####################

# Create molecule named MS1
createMolecule MS2

# Create MEF-1 from MET-10
createResidue MEF in MS2
addToResidue /NAME/MS2/MEF /NAME/1/MET-10 not bb

# Create CYF-2 from CYM-102
createResidue CYF in MS2
addToResidue /NAME/MS2/CYF /NAME/1/CYM-102 not bb

# Create GLT-3 from GLU-105
createResidue GLT in MS2
addToResidue /NAME/MS2/GLT /NAME/1/GLU-105 not bb

# Create HIT-4 from HID-106
createResidue HIT in MS2
addToResidue /NAME/MS2/HIT /NAME/1/HID-106 not bb

# Create FE2-5 from FE-500
createResidue FE2 in MS2
addToResidue /NAME/MS2/FE2 /NAME/2/.FE-500/FE..

# Create OH1-6 from MOH-600
createResidue OH1 in MS2
addToResidue /NAME/MS2/OH1 /NAME/3/MOH-600 not bb

# Methyl terminating groups (Add these after all other residue have been added)

addFragment terminal/CH3 bd /NAME/MS2/MEF-1/.CB. ag /NAME/MS2/MEF-1/.CG. tr /NAME/MS2/MEF-1/.SD. 47.88
addFragment terminal/CH3 bd /NAME/MS2/CYF-2/.N.. ag /NAME/MS2/CYF-2/.CA. tr /NAME/MS2/CYF-2/.C.. 114.43
addFragment terminal/CH3 bd /NAME/MS2/GLT-3/.CB. ag /NAME/MS2/GLT-3/.CG. tr /NAME/MS2/GLT-3/.CD. 346.3
addFragment terminal/CH3 bd /NAME/MS2/HIT-4/.CB. ag /NAME/MS2/HIT-4/.CG. tr /NAME/MS2/HIT-4/.ND1 245.56

# Create bonds with FE1 
createBond /NAME/MS2/FE2/FE.. /NAME/MS2/MEF/.SD.
createBond /NAME/MS2/FE2/FE.. /NAME/MS2/CYF/.SG.
createBond /NAME/MS2/FE2/FE.. /NAME/MS2/CYF/.O..
createBond /NAME/MS2/FE2/FE.. /NAME/MS2/GLT/.OE1
createBond /NAME/MS2/FE2/FE.. /NAME/MS2/HIT/.NE2
createBond /NAME/MS2/FE2/FE.. /NAME/MS2/OH1/.O..

# Atomtype 
atomType /NAME/MS2

# Assign bonds and angles
assignParameters /NAME/MS2

# Add Bond and Angle Parameters
addBondAndAngleParameters /NAME/MS2 NAME

# Write FRCMOD file
writeParams NAME NAME_params.xml

# Write pdb/mol files
writePdb /NAME/MS2 NAME_sidechain.pdb
writeMol /NAME/MS2 NAME_sidechain.mol
writeSdf /NAME/MS2 NAME_sidechain.sdf

# Gaussian options
levelOfTheory B3LYP
basisSet 6-311G*
clusterCharge MS2 0
clusterSpin 1
gaussianNProc 8
gaussianMem 3000MB

# Set g09 input name --> Optimize and get force constants
gaussianOptAndFC /NAME/MS2 NAME_sidechain.com

# Exit MCPB
quit