# LOAD FORCE FIELD

source leaprc.ff99SB
source leaprc.gaff

addAtomTypes {
{"FE" "FE" "sp3"}
{"SF" "S" "sp3"}
{"SM" "S" "sp3"}
}



# LOAD MANGANESE CENTER PARAMETERS

frcmod=loadamberparams CC[C]2_Fe-III.frcmod

loadoff FE.off
loadoff CY1.off
loadoff CY2.off
loadoff CY3.off



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



# SAVING PARAMETERS WITH NO COUNTERIONS OR SOLVATEBOX

saveamberparm desulforedoxin  CC[C]2_Fe-III.prmtop CC[C]2_Fe-III.inpcrd



# DEFINE CONNECTIVITY MANGANESE-LIGAND
## bond <unit>.<residue1>.<atom type1> <unit>.<residue2>.<atom type2>
bond desulforedoxin.73.FE desulforedoxin.9.SF
bond desulforedoxin.73.FE desulforedoxin.12.SF
bond desulforedoxin.73.FE desulforedoxin.28.SM
bond desulforedoxin.73.FE desulforedoxin.29.SM

bond desulforedoxin.74.FE desulforedoxin.45.SF
bond desulforedoxin.74.FE desulforedoxin.48.SF
bond desulforedoxin.74.FE desulforedoxin.64.SM
bond desulforedoxin.74.FE desulforedoxin.65.SM



# ADD COUNTERIONS

addions desulforedoxin Na+ 0
addions desulforedoxin Cl- 0



# ADD SOLVATEBOX

solvateoct desulforedoxin TIP3PBOX 10.0



# CHECK UNIT

check desulforedoxin



# SAVE PARAMETERS

saveamberparm desulforedoxin  CC[C]2_Fe-III.prmtop CC[C]2_Fe-III.inpcrd

