source oldff/leaprc.ff14SB
source leaprc.gaff
addAtomTypes {
        { "M1"  "Zn" "sp3" }
        { "Y1"  "N" "sp3" }
        { "Y2"  "N" "sp3" }
        { "Y3"  "N" "sp3" }
        { "Y4"  "N" "sp3" }
}
HD1 = loadmol2 HD1.mol2
HD2 = loadmol2 HD2.mol2
HE1 = loadmol2 HE1.mol2
ZN1 = loadmol2 ZN1.mol2
MS1 = loadmol2 MS1.mol2
loadamberparams MNS.frcmod
loadamberparams frcmod.ions1lm_126_tip3p
loadamberparams 1OKL_mcpbpy.frcmod
mol = loadpdb 1OKL_mcpbpy.pdb
bond mol.90.NE2 mol.256.ZN
bond mol.92.NE2 mol.256.ZN
bond mol.115.ND1 mol.256.ZN
bond mol.256.ZN mol.257.N3S
bond mol.89.C mol.90.N
bond mol.90.C mol.91.N
bond mol.91.C mol.92.N
bond mol.92.C mol.93.N
bond mol.114.C mol.115.N
bond mol.115.C mol.116.N
savepdb mol 1OKL_dry.pdb
saveamberparm mol 1OKL_dry.prmtop 1OKL_dry.inpcrd
solvatebox mol TIP3PBOX 10.0
addions mol Na+ 0
addions mol Cl- 0
savepdb mol 1OKL_solv.pdb
saveamberparm mol 1OKL_solv.prmtop 1OKL_solv.inpcrd
quit
 
