source leaprc.protein.ff19SB
source leaprc.gaff
source leaprc.water.opc
addAtomTypes {
        { "M1"  "Ni" "sp3" }
        { "M2"  "Ni" "sp3" }
        { "Y1"  "O" "sp3" }
        { "Y2"  "N" "sp3" }
        { "Y3"  "N" "sp3" }
        { "Y4"  "N" "sp3" }
        { "Y5"  "N" "sp3" }
        { "Y6"  "O" "sp3" }
        { "Y7"  "O" "sp3" }
}
HD1 = loadmol2 HD1.mol2
HD2 = loadmol2 HD2.mol2
KX1 = loadmol2 KX1.mol2
HE1 = loadmol2 HE1.mol2
HD3 = loadmol2 HD3.mol2
AP1 = loadmol2 AP1.mol2
NI1 = loadmol2 NI1.mol2
NI2 = loadmol2 NI2.mol2
loadamberparams KCX.frcmod
loadamberparams frcmod.ionslm_126_opc
loadamberparams 6rkg_mcpbpy.frcmod
mol = loadpdb 6rkg_mcpbpy.pdb
bond mol.359.NE2 mol.794.NI
bond mol.361.NE2 mol.794.NI
bond mol.442.OQ1 mol.793.NI
bond mol.442.OQ2 mol.794.NI
bond mol.471.ND1 mol.793.NI
bond mol.497.NE2 mol.793.NI
bond mol.585.OD1 mol.794.NI
bond mol.358.C mol.359.N
bond mol.359.C mol.360.N
bond mol.360.C mol.361.N
bond mol.361.C mol.362.N
bond mol.441.C mol.442.N
bond mol.442.C mol.443.N
bond mol.470.C mol.471.N
bond mol.471.C mol.472.N
bond mol.496.C mol.497.N
bond mol.497.C mol.498.N
bond mol.584.C mol.585.N
bond mol.585.C mol.586.N
savepdb mol 6rkg_dry.pdb
saveamberparm mol 6rkg_dry.prmtop 6rkg_dry.inpcrd
solvatebox mol OPCBOX 10.0
addions mol Na+ 0
addions mol Cl- 0
savepdb mol 6rkg_solv.pdb
saveamberparm mol 6rkg_solv.prmtop 6rkg_solv.inpcrd
quit
 
