source leaprc.ff14SB
source leaprc.gaff
addAtomTypes {
        { "X1"  "N" "sp3" }
        { "X2"  "N" "sp3" }
        { "X3"  "N" "sp3" }
        { "Z1"  "Zn" "sp3" }
        { "X4"  "N" "sp3" }
}
loadoff atomic_ions.lib
loadamberparams frcmod.ions1lsm_hfe_tip3p
HD1 = loadmol2 HD1.mol2
HD2 = loadmol2 HD2.mol2
HE1 = loadmol2 HE1.mol2
ZN1 = loadmol2 ZN1.mol2
MS1 = loadmol2 MS1.mol2
loadamberparams MNS.frcmod
loadamberparams 1OKL.frcmod
mol = loadpdb 1OKL_mcpbpy.pdb
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_rnb_dry.pdb
saveamberparm mol 1OKL_rnb_dry.prmtop 1OKL_rnb_dry.inpcrd
solvatebox mol TIP3PBOX 10.0
addions mol Na+ 0
addions mol Cl- 0
savepdb mol 1OKL_rnb_solv.pdb
saveamberparm mol 1OKL_rnb_solv.prmtop 1OKL_rnb_solv.inpcrd
quit
 
