# 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"}
{"W1" "O" "sp3"}
{"HM" "H" "s"}
}



# LOAD MANGANESE CENTER PARAMETERS

frcmod=loadamberparams HHDHW_Mn-III.frcmod

loadoff M01.off
loadoff H01.off
loadoff H02.off
loadoff H03.off
loadoff D01.off
loadoff WAA.off



# CREATE ENZYME UNIT
## <unit> = loadpdb <please refer to the respective PDB file>
MnSOD = loadpdb 1N0J.pdb



# SAVING PARAMETERS WITH NO COUNTERIONS OR SOLVATEBOX

saveamberparm MnSOD  HHDHW_Mn-III.prmtop HHDHW_Mn-III.inpcrd



# DEFINE CONNECTIVITY MANGANESE-LIGAND
## bond <unit>.<residue1>.<atom type1> <unit>.<residue2>.<atom type2>
bond MnSOD.397.M1 MnSOD.26.NI 
bond MnSOD.397.M1 MnSOD.74.NJ 
bond MnSOD.397.M1 MnSOD.163.NK 
bond MnSOD.397.M1 MnSOD.159.D1 
bond MnSOD.397.M1 MnSOD.493.W1

bond MnSOD.398.M1 MnSOD.224.NI 
bond MnSOD.398.M1 MnSOD.272.NJ 
bond MnSOD.398.M1 MnSOD.361.NK 
bond MnSOD.398.M1 MnSOD.357.D1 
bond MnSOD.398.M1 MnSOD.567.W1



# 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  HHDHW_Mn-III.prmtop HHDHW_Mn-III.inpcrd

