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

addAtomTypes {
{"M1" "Mn" "sp3d2"}
{"NW" "O" "sp2"}
{"D1" "O" "sp3"}
{"E1" "O" "sp3"}
{"W1" "O" "sp3"}
{"W2" "O" "sp3"}
{"W3" "O" "sp3"}
{"HM" "H" "s"}
}



# LOAD MANGANESE CENTER PARAMETERS

frcmod=loadamberparams DENWWW_Mn-II.frcmod

loadoff M12.off
loadoff N01.off
loadoff D13.off
loadoff E10.off
loadoff WAK.off
loadoff WAL.off
loadoff WAM.off



# CREATE ENZYME UNIT
## <unit> = loadpdb <please refer to the respective PDB file>
GluDH = loadpdb 3NXL.pdb



# SAVING PARAMETERS WITH NO COUNTERIONS OR SOLVATEBOX

saveamberparm GluDH  DENWWW_Mn-II.prmtop DENWWW_Mn-II.inpcrd



# DEFINE CONNECTIVITY MANGANESE-LIGAND
## bond <unit>.<residue1>.<atom type1> <unit>.<residue2>.<atom type2>
bond GluDH.1656.M1 GluDH.271.NW
bond GluDH.1656.M1 GluDH.218.D1
bond GluDH.1656.M1 GluDH.243.E1
bond GluDH.1656.M1 GluDH.1673.W1
bond GluDH.1656.M1 GluDH.1906.W2
bond GluDH.1656.M1 GluDH.1907.W3

bond GluDH.1657.M1 GluDH.681.NW
bond GluDH.1657.M1 GluDH.628.D1
bond GluDH.1657.M1 GluDH.653.E1
bond GluDH.1657.M1 GluDH.1925.W1
bond GluDH.1657.M1 GluDH.2057.W2
bond GluDH.1657.M1 GluDH.2068.W3

bond GluDH.1658.M1 GluDH.1093.NW
bond GluDH.1658.M1 GluDH.1040.D1
bond GluDH.1658.M1 GluDH.1065.E1
bond GluDH.1658.M1 GluDH.2131.W1
bond GluDH.1658.M1 GluDH.2204.W2
bond GluDH.1658.M1 GluDH.2226.W3

bond GluDH.1659.M1 GluDH.1505.NW
bond GluDH.1659.M1 GluDH.1452.D1
bond GluDH.1659.M1 GluDH.1477.E1
bond GluDH.1659.M1 GluDH.2329.W1
bond GluDH.1659.M1 GluDH.2488.W2
bond GluDH.1659.M1 GluDH.2531.W3



# ADD COUNTERIONS

addions2 GluDH Na+ 0
addions2 GluDH Cl- 0



# ADD SOLVATEBOX

solvatebox GluDH TIP3PBOX 12.0



# CHECK UNIT

check GluDH



# SAVE PARAMETERS

saveamberparm GluDH  DENWWW_Mn-II.prmtop DENWWW_Mn-II.inpcrd

