source leaprc.protein.ff19SB
source leaprc.water.opc
addAtomTypes {
        { "M1"  "Fe" "sp3" }
        { "Y1"  "C" "sp3" }
        { "Y2"  "C" "sp3" }
        { "Y3"  "C" "sp3" }
        { "Y4"  "C" "sp3" }
        { "Y6"  "C" "sp3" }
        { "Y7"  "C" "sp3" }
        { "Y8"  "C" "sp3" }
        { "Y9"  "C" "sp3" }
        { "Z1"  "C" "sp3" }
}
LG1 = loadmol2 LG1.mol2
FE1 = loadmol2 FE1.mol2
SL1 = loadmol2 SL1.mol2
loadamberparams LRG.frcmod
loadamberparams SML.frcmod
loadamberparams frcmod.ionslm_126_opc
loadamberparams TEST_mcpbpy.frcmod
mol = loadpdb TEST_mcpbpy.pdb
bond mol.1.C5 mol.2.FE
bond mol.1.C5 mol.2.FE
bond mol.1.C6 mol.2.FE
bond mol.1.C6 mol.2.FE
bond mol.1.C7 mol.2.FE
bond mol.1.C7 mol.2.FE
bond mol.1.C8 mol.2.FE
bond mol.1.C8 mol.2.FE
bond mol.1.C9 mol.2.FE
bond mol.1.C9 mol.2.FE
bond mol.1.C9 mol.2.FE
bond mol.1.C9 mol.2.FE
bond mol.2.FE mol.3.C10
bond mol.2.FE mol.3.C10
bond mol.2.FE mol.3.C11
bond mol.2.FE mol.3.C11
bond mol.2.FE mol.3.C12
bond mol.2.FE mol.3.C12
bond mol.2.FE mol.3.C13
bond mol.2.FE mol.3.C13
savepdb mol TEST_dry.pdb
saveamberparm mol TEST_dry.prmtop TEST_dry.inpcrd
solvatebox mol OPCBOX 10.0
addions mol Na+ 0
addions mol Cl- 0
savepdb mol TEST_solv.pdb
saveamberparm mol TEST_solv.prmtop TEST_solv.inpcrd
quit
 
