# LOAD FORCE FIELD

source leaprc.ff99SB
source leaprc.gaff

addAtomTypes {
{"FE" "FE" "sp3"}
{"S" "S" "sp3"}
{"SX" "S" "sp3"}
}



# LOAD MANGANESE CENTER PARAMETERS

frcmod=loadamberparams CC[FE2]SS[FE2]CC_Fe-III.frcmod

loadoff FES.off
loadoff CY1.off



# CREATE ENZYME UNIT
## <unit> = loadpdb <please refer to the respective PDB file>
ferrodoxin = loadpdb 4FXC.pdb



# SAVING PARAMETERS WITH NO COUNTERIONS OR SOLVATEBOX

saveamberparm ferrodoxin  CC[FE2]SS[FE2]CC_Fe-III.prmtop CC[FE2]SS[FE2]CC_Fe-III.inpcrd



# DEFINE CONNECTIVITY MANGANESE-LIGAND
## bond <unit>.<residue1>.<atom type1> <unit>.<residue2>.<atom type2>
bond ferrodoxin.99.FE1 ferrodoxin.41.SX
bond ferrodoxin.99.FE1 ferrodoxin.46.SX

bond ferrodoxin.99.FE2 ferrodoxin.49.SX
bond ferrodoxin.99.FE2 ferrodoxin.79.SX



# ADD COUNTERIONS

addions ferrodoxin Na+ 0
addions ferrodoxin Cl- 0



# ADD SOLVATEBOX

solvateoct ferrodoxin TIP3PBOX 10.0



# CHECK UNIT

check ferrodoxin



# SAVE PARAMETERS

saveamberparm ferrodoxin  CC[FE2]SS[FE2]CC_Fe-III.prmtop CC[FE2]SS[FE2]CC_Fe-III.inpcrd

