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

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



# LOAD MANGANESE CENTER PARAMETERS

frcmod=loadamberparams HHEWW_Mn-II.frcmod

loadoff M06.off
loadoff H11.off
loadoff H12.off
loadoff E03.off
loadoff WAG.off
loadoff WAH.off



# CREATE ENZYME UNIT
## <unit> = loadpdb <please refer to the respective PDB file>
MndD = loadpdb 1F1U.pdb



# SAVING PARAMETERS WITH NO COUNTERIONS OR SOLVATEBOX

saveamberparm MndD  HHEWW_Mn-II.prmtop HHEWW_Mn-II.inpcrd



# DEFINE CONNECTIVITY MANGANESE-LIGAND
## bond <unit>.<residue1>.<atom type1> <unit>.<residue2>.<atom type2>
bond MndD.645.M1 MndD.155.NI 
bond MndD.645.M1 MndD.214.NJ 
bond MndD.645.M1 MndD.267.E1 
bond MndD.645.M1 MndD.988.W1
bond MndD.645.M1 MndD.989.W2

bond MndD.646.M1 MndD.476.NI 
bond MndD.646.M1 MndD.535.NJ 
bond MndD.646.M1 MndD.588.E1
bond MndD.646.M1 MndD.1307.W1
bond MndD.646.M1 MndD.1308.W2



# ADD COUNTERIONS

addions2 MndD Na+ 0
addions2 MndD Cl- 0



# ADD SOLVATEBOX

solvatebox MndD TIP3PBOX 12.0



# CHECK UNIT

check MndD



# SAVE PARAMETERS

saveamberparm MndD HHEWW_Mn-II.prmtop HHEWW_Mn-II.inpcrd

