# LOAD FORCE FIELD
source leaprc.ff99
source leaprc.gaff

addAtomTypes {
{"M1" "Mn" "sp3d2"}
{"D1" "O" "sp3"}
{"E1" "O" "sp3"}
{"R1" "O" "sp3"}
{"R2" "O" "sp3"}
{"W1" "O" "sp3"}
{"W2" "O" "sp3"}
{"HM" "H" "s"}
}



# LOAD MANGANESE CENTER PARAMETERS

frcmod=loadamberparams ED[PY2]WW_Mn-II.frcmod

loadoff M05.off
loadoff D05.off
loadoff E02.off
loadoff PYA.off
loadoff WAE.off
loadoff WAF.off



# CREATE ENZYME UNIT
## <unit> = loadpdb <please refer to the respective PDB file>
pyrKin = loadpdb 2G50.pdb



# SAVING PARAMETERS WITH NO COUNTERIONS OR SOLVATEBOX

saveamberparm pyrKin  ED[PY2]WW_Mn-II.prmtop ED[PY2]WW_Mn-II.inpcrd



# DEFINE CONNECTIVITY MANGANESE-LIGAND
## bond <unit>.<residue1>.<atom type1> <unit>.<residue2>.<atom type2>
bond pyrKin.4158.M1 pyrKin.283.D1 
bond pyrKin.4158.M1 pyrKin.263.E1
bond pyrKin.4158.M1 pyrKin.4159.R1
bond pyrKin.4158.M1 pyrKin.4159.R2
bond pyrKin.4158.M1 pyrKin.4149.W1
bond pyrKin.4158.M1 pyrKin.4150.W2

bond pyrKin.4160.M1 pyrKin.798.D1 
bond pyrKin.4160.M1 pyrKin.774.E1
bond pyrKin.4160.M1 pyrKin.4161.R1
bond pyrKin.4160.M1 pyrKin.4161.R2
bond pyrKin.4160.M1 pyrKin.4151.W1
bond pyrKin.4160.M1 pyrKin.4152.W2

bond pyrKin.4162.M1 pyrKin.1310.D1 
bond pyrKin.4162.M1 pyrKin.1286.E1
bond pyrKin.4162.M1 pyrKin.4163.R1
bond pyrKin.4162.M1 pyrKin.4163.R2
bond pyrKin.4162.M1 pyrKin.4153.W1
bond pyrKin.4162.M1 pyrKin.4154.W2

bond pyrKin.4164.M1 pyrKin.1831.D1 
bond pyrKin.4164.M1 pyrKin.1807.E1
bond pyrKin.4164.M1 pyrKin.4165.R1
bond pyrKin.4164.M1 pyrKin.4165.R2
bond pyrKin.4164.M1 pyrKin.4155.W1
bond pyrKin.4164.M1 pyrKin.4156.W2

bond pyrKin.4166.M1 pyrKin.2352.D1 
bond pyrKin.4166.M1 pyrKin.2328.E1
bond pyrKin.4166.M1 pyrKin.4167.R1
bond pyrKin.4166.M1 pyrKin.4167.R2
bond pyrKin.4166.M1 pyrKin.4157.W1
bond pyrKin.4166.M1 pyrKin.4158.W2

bond pyrKin.4168.M1 pyrKin.2867.D1 
bond pyrKin.4168.M1 pyrKin.2843.E1
bond pyrKin.4168.M1 pyrKin.4169.R1
bond pyrKin.4168.M1 pyrKin.4169.R2
bond pyrKin.4168.M1 pyrKin.4159.W1
bond pyrKin.4168.M1 pyrKin.4160.W2

bond pyrKin.4170.M1 pyrKin.3377.D1 
bond pyrKin.4170.M1 pyrKin.3353.E1
bond pyrKin.4170.M1 pyrKin.4171.R1
bond pyrKin.4170.M1 pyrKin.4171.R2
bond pyrKin.4170.M1 pyrKin.4161.W1
bond pyrKin.4170.M1 pyrKin.4162.W2

bond pyrKin.4172.M1 pyrKin.3896.D1 
bond pyrKin.4172.M1 pyrKin.3872.E1
bond pyrKin.4172.M1 pyrKin.4173.R1
bond pyrKin.4172.M1 pyrKin.4173.R2
bond pyrKin.4172.M1 pyrKin.4163.W1
bond pyrKin.4172.M1 pyrKin.4164.W2



# ADD COUNTERIONS

addions2 pyrKin Na+ 0
addions2 pyrKin Cl- 0



# ADD SOLVATEBOX

solvatebox pyrKin TIP3PBOX 12.0



# CHECK UNIT

check pyrKin



# SAVE PARAMETERS

saveamberparm pyrKin  ED[PY2]WW_Mn-II.prmtop ED[PY2]WW_Mn-II.inpcrd

