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

addAtomTypes {
{"M1" "Mn" "sp3d2"}
{"NI" "N" "sp2"}
{"D1" "O" "sp3"}
{"E1" "O" "sp3"}
{"W1" "O" "sp3"}
{"W2" "O" "sp3"}
{"W3" "O" "sp3"}
{"HM" "H" "s"}
}



# LOAD MANGANESE CENTER PARAMETERS

frcmod=loadamberparams HDEWWW_Mn-II.frcmod

loadoff M04.off
loadoff H10.off
loadoff D04.off
loadoff E01.off
loadoff WAB.off
loadoff WAC.off
loadoff WAD.off



# CREATE ENZYME UNIT
## <unit> = loadpdb <please refer to the respective PDB file>
citC = loadpdb 3HB3.pdb



# SAVING PARAMETERS WITH NO COUNTERIONS OR SOLVATEBOX

saveamberparm citC  HDEWWW_Mn-II.prmtop HDEWWW_Mn-II.inpcrd



# DEFINE CONNECTIVITY MANGANESE-LIGAND
## bond <unit>.<residue1>.<atom type1> <unit>.<residue2>.<atom type2>~
bond citC.1024.M1 citC.403.NI 
bond citC.1024.M1 citC.404.D1
bond citC.1024.M1 citC.763.E1
bond citC.1024.M1 citC.1026.W1
bond citC.1024.M1 citC.1184.W2
bond citC.1024.M1 citC.1311.W3



# ADD COUNTERIONS

addions2 citC Na+ 0
addions2 citC Cl- 0



# ADD SOLVATEBOX

solvatebox citC TIP3PBOX 12.0



# CHECK UNIT

check citC



# SAVE PARAMETERS

saveamberparm citC  HDEWWW_Mn-II.prmtop HDEWWW_Mn-II.inpcrd

