# LOAD FORCE FIELD

source leaprc.ff99SB
source leaprc.gaff

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



# LOAD MANGANESE CENTER PARAMETERS

frcmod=loadamberparams CCCC_Fe-III.frcmod

loadoff FE.off
loadoff CY1.off



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



# SAVING PARAMETERS WITH NO COUNTERIONS OR SOLVATEBOX

saveamberparm rubredoxin  CCCC_Fe-III.prmtop CCCC_Fe-III.inpcrd



# DEFINE CONNECTIVITY MANGANESE-LIGAND
## bond <unit>.<residue1>.<atom type1> <unit>.<residue2>.<atom type2>
bond rubredoxin.54.FE rubredoxin.6.SF
bond rubredoxin.54.FE rubredoxin.9.SF
bond rubredoxin.54.FE rubredoxin.39.SF
bond rubredoxin.54.FE rubredoxin.42.SF



# ADD COUNTERIONS

addions rubredoxin Na+ 0
addions rubredoxin Cl- 0



# ADD SOLVATEBOX

solvateoct rubredoxin TIP3PBOX 10.0



# CHECK UNIT

check rubredoxin



# SAVE PARAMETERS

saveamberparm rubredoxin  CCCC_Fe-III.prmtop CCCC_Fe-III.inpcrd

