# LOAD FORCE FIELD

source leaprc.ff99
source leaprc.gaff

addAtomTypes {
{"M1" "Mn" "sp3d2"}
{"D1" "O" "sp2"}
{"D2" "O" "sp3"}
{"W1" "O" "sp3"}
{"W2" "O" "sp3"}
{"W3" "O" "sp3"}
{"W4" "O" "sp3"}
{"HM" "H" "s"}
}



# LOAD MANGANESE CENTER PARAMETERS

frcmod=loadamberparams DDWWWW_Mn-II.frcmod

loadoff M13.off
loadoff D14.off
loadoff D15.off
loadoff WAN.off
loadoff WAO.off
loadoff WAP.off
loadoff WAQ.off



# CREATE ENZYME UNIT
## <unit> = loadpdb <please refer to the respective PDB file>
int = loadpdb 1A5V.pdb 



# SAVING PARAMETERS WITH NO COUNTERIONS OR SOLVATEBOX

saveamberparm int  DDWWWW_Mn-II.prmtop DDWWWW_Mn-II.inpcrd



# DEFINE CONNECTIVITY MANGANESE-LIGAND
## bond <unit>.<residue1>.<atom type1> <unit>.<residue2>.<atom type2>
bond int.200.M1 int.64.D1
bond int.200.M1 int.121.D2
bond int.200.M1 int.201.W1
bond int.200.M1 int.202.W2
bond int.200.M1 int.203.W3
bond int.200.M1 int.204.W4



# ADD COUNTERIONS

addions2 int Na+ 0
addions2 int Cl- 0


# ADD SOLVATEBOX

solvatebox int TIP3PBOX 12.0


# CHECK UNIT

check int


# SAVE PARAMETERS

saveamberparm int  DDWWWW_Mn-II.prmtop DDWWWW_Mn-II.inpcrd

