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

addAtomTypes {
{"M1" "Mn" "sp3d"}
{"NI" "N" "sp3"}
{"NJ" "N" "sp3"}
{"D1" "O" "sp3"}
{"D2" "O" "sp3"}
{"E1" "O" "sp3"}
{"HM" "H" "s"}
}



# LOAD MANGANESE CENTER PARAMETERS

frcmod=loadamberparams HHE[D2]_Mn-II.frcmod

loadoff M09.off
loadoff H15.off
loadoff H16.off
loadoff D07.off
loadoff E07.off



# CREATE ENZYME UNIT
## <unit> = loadpdb <please refer to the respective PDB file>
psaA = loadpdb 1PSZ.pdb



# SAVING PARAMETERS WITH NO COUNTERIONS OR SOLVATEBOX

saveamberparm psaA  HHE[D2]_Mn-II.prmtop HHE[D2]_Mn-II.inpcrd



# DEFINE CONNECTIVITY MANGANESE-LIGAND
## bond <unit>.<residue1>.<atom type1> <unit>.<residue2>.<atom type2>
bond psaA.310.M1 psaA.67.NI
bond psaA.310.M1 psaA.139.NJ
bond psaA.310.M1 psaA.280.D1
bond psaA.310.M1 psaA.280.D2
bond psaA.310.M1 psaA.205.E1



# ADD COUNTERIONS

addions2 psaA Na+ 0
addions2 psaA Cl- 0



# ADD SOLVATEBOX

solvatebox psaA TIP3PBOX 12.0



# CHECK UNIT

check psaA



# SAVE PARAMETERS

saveamberparm psaA HHE[D2]_Mn-II.prmtop HHE[D2]_Mn-II.inpcrd

