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

addAtomTypes {
{"M1" "Mn" "sp3d2"}
{"NI" "N" "sp2"}
{"NJ" "N" "sp2"}
{"NK" "N" "sp2"}
{"D1" "O" "sp3"}
{"R1" "O" "sp2"}
{"W1" "O" "sp3"}
{"HM" "H" "s"}
}



# LOAD MANGANESE CENTER PARAMETERS

frcmod=loadamberparams HHDH[HO]O_Mn-III.frcmod

loadoff M03.off
loadoff H07.off
loadoff H08.off
loadoff H09.off
loadoff D03.off
loadoff HOB.off
loadoff OOA.off



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



# SAVING PARAMETERS WITH NO COUNTERIONS OR SOLVATEBOX

saveamberparm MnSOD  HHDH[HO]O_Mn-III.prmtop HHDH[HO]O_Mn-III.inpcrd



# DEFINE CONNECTIVITY MANGANESE-LIGAND
## bond <unit>.<residue1>.<atom type1> <unit>.<residue2>.<atom type2>
bond MnSOD.407.M1 MnSOD.28.NI 
bond MnSOD.407.M1 MnSOD.83.NJ 
bond MnSOD.407.M1 MnSOD.170.NK 
bond MnSOD.407.M1 MnSOD.166.D1 
bond MnSOD.407.M1 MnSOD.411.W1
bond MnSOD.407.M1 MnSOD.408.R1

bond MnSOD.409.M1 MnSOD.231.NI 
bond MnSOD.409.M1 MnSOD.286.NJ 
bond MnSOD.409.M1 MnSOD.373.NK 
bond MnSOD.409.M1 MnSOD.369.D1 
bond MnSOD.409.M1 MnSOD.506.W1
bond MnSOD.409.M1 MnSOD.410.R1



# ADD COUNTERIONS

addions2 MnSOD Na+ 0
addions2 MnSOD Cl- 0



# ADD SOLVATEBOX

solvatebox MnSOD TIP3PBOX 12.0



# CHECK UNIT

check MnSOD



# SAVE PARAMETERS

saveamberparm MnSOD  HHDH[HO]O_Mn-III.prmtop HHDH[HO]O_Mn-III.inpcrd

