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

addAtomTypes {
{"M1" "Mn" "sp3"}
{"D1" "O" "sp2"}
{"D2" "O" "sp3"}
{"E1" "O" "sp3"}
{"R1" "Cl" "sp3"}
}



# LOAD MANGANESE CENTER PARAMETERS

frcmod=loadamberparams DED[CL]_Mn-II.frcmod

loadoff M10.off
loadoff D09.off
loadoff D10.off
loadoff E08.off
loadoff CLA.off



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



# SAVING PARAMETERS WITH NO COUNTERIONS OR SOLVATEBOX

saveamberparm ClMucCyiso  DED[CL]_Mn-II.prmtop DED[CL]_Mn-II.inpcrd



# DEFINE CONNECTIVITY MANGANESE-LIGAND
## bond <unit>.<residue1>.<atom type1> <unit>.<residue2>.<atom type2>
bond ClMucCyiso.371.M1 ClMucCyiso.194.D1 
bond ClMucCyiso.371.M1 ClMucCyiso.245.D2
bond ClMucCyiso.371.M1 ClMucCyiso.220.E1
bond ClMucCyiso.371.M1 ClMucCyiso.372.R1



# ADD COUNTERIONS

addions2 ClMucCyiso Na+ 0
addions2 ClMucCyiso Cl- 0



# ADD SOLVATEBOX

solvatebox ClMucCyiso TIP3PBOX 12.0



# CHECK UNIT

check ClMucCyiso



# SAVE PARAMETERS

saveamberparm ClMucCyiso  DED[CL]_Mn-II.prmtop DED[CL]_Mn-II.inpcrd

