# LOAD FORCE FIELD
source leaprc.ff99
source leaprc.gaff

addAtomTypes {
{"M1" "Mn" "sp3d"}
{"D1" "O" "sp3"}
{"E1" "O" "sp3"}
{"E2" "O" "sp3"}
{"R1" "O" "sp3"}
{"R2" "O" "sp3"}
}



# LOAD MANGANESE CENTER PARAMETERS

frcmod=loadamberparams DEE[SO2]_Mn-II.frcmod

loadoff M08.off
loadoff D06.off
loadoff E05.off
loadoff E06.off
loadoff SOA.off



# CREATE ENZYME UNIT
## <unit> = loadpdb <please refer to the respective PDB file>
MndRac = loadpdb 2MNR.pdb



# SAVING PARAMETERS WITH NO COUNTERIONS OR SOLVATEBOX

saveamberparm MndRac  DEE[SO2]_Mn-II.prmtop DEE[SO2]_Mn-II.inpcrd



# DEFINE CONNECTIVITY MANGANESE-LIGAND
## bond <unit>.<residue1>.<atom type1> <unit>.<residue2>.<atom type2>
bond MndRac.360.M1 MndRac.195.D1 
bond MndRac.360.M1 MndRac.221.E1 
bond MndRac.360.M1 MndRac.247.E2 
bond MndRac.360.M1 MndRac.361.R1
bond MndRac.360.M1 MndRac.361.R2



# ADD COUNTERIONS

addions2 MndRac Na+ 0
addions2 MndRac Cl- 0



# ADD SOLVATEBOX

solvatebox MndRac TIP3PBOX 12.0



# CHECK UNIT

check MndRac



# SAVE PARAMETERS

saveamberparm MndRac  DEE[SO2]_Mn-II.prmtop DEE[SO2]_Mn-II.inpcrd

