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

addAtomTypes {
{"M1" "Mn" "sp3d2"}
{"D1" "O" "sp2"}
{"D2" "O" "sp3"}
{"E1" "O" "sp3"}
{"W1" "O" "sp3"}
{"W2" "O" "sp3"}
{"W3" "O" "sp3"}
{"HM" "H" "s"}
}



# LOAD MANGANESE CENTER PARAMETERS

frcmod=loadamberparams DEDWWW_Mn-II.frcmod

loadoff M14.off
loadoff D16.off
loadoff D17.off
loadoff E11.off
loadoff WAR.off
loadoff WAS.off
loadoff WAU.off



# CREATE ENZYME UNIT
## <unit> = loadpdb <please refer to the respective PDB file>
MucCyiso = loadpdb 3CT2.pdb 



# SAVING PARAMETERS WITH NO COUNTERIONS OR SOLVATEBOX

saveamberparm MucCyiso  DEDWWW_Mn-II.prmtop DEDWWW_Mn-II.inpcrd



# DEFINE CONNECTIVITY MANGANESE-LIGAND
## bond <unit>.<residue1>.<atom type1> <unit>.<residue2>.<atom type2>
bond MucCyiso.726.M1 MucCyiso.189.D1
bond MucCyiso.726.M1 MucCyiso.240.D2
bond MucCyiso.726.M1 MucCyiso.215.E1
bond MucCyiso.726.M1 MucCyiso.772.W1
bond MucCyiso.726.M1 MucCyiso.898.W2
bond MucCyiso.726.M1 MucCyiso.899.W3

bond MucCyiso.727.M1 MucCyiso.550.D1
bond MucCyiso.727.M1 MucCyiso.601.D2
bond MucCyiso.727.M1 MucCyiso.576.E1
bond MucCyiso.727.M1 MucCyiso.946.W1
bond MucCyiso.727.M1 MucCyiso.1049.W2
bond MucCyiso.727.M1 MucCyiso.1130.W3



# ADD COUNTERIONS

addions2 MucCyiso Na+ 0
addions2 MucCyiso Cl- 0



# ADD SOLVATEBOX

solvatebox MucCyiso TIP3PBOX 12.0



# CHECK UNIT

check MucCyiso



# SAVE PARAMETERS

saveamberparm MucCyiso DEDWWW_Mn-II.prmtop DEDWWW_Mn-II.inpcrd

