source oldff/leaprc.ff14SB
source leaprc.gaff
addAtomTypes {
        { "X1"  "S" "sp3" }
        { "X2"  "S" "sp3" }
        { "X3"  "N" "sp3" }
        { "X4"  "S" "sp3" }
        { "Z1"  "As" "sp3" }
}
CS1 = loadmol2 CS1.mol2
loadamberparams CS1.frcmod
CS2 = loadmol2 CS2.mol2
loadamberparams CS2.frcmod
VL1 = loadmol2 VL1.mol2
loadamberparams VL1.frcmod
CS3 = loadmol2 CS3.mol2
loadamberparams CS3.frcmod
AS1 = loadmol2 AS1.mol2
loadamberparams AS1.frcmod
loadamberparams frcmod.ions1lm_126_tip3p
loadamberparams ArsD_mcpbpy.frcmod
mol = loadpdb ArsD_mcpbpy.pdb
bond mol.12.SG mol.121.AS
bond mol.13.SG mol.121.AS
bond mol.17.N mol.121.AS
bond mol.18.SG mol.121.AS
bond mol.11.C mol.12.N
bond mol.12.C mol.13.N
bond mol.13.C mol.14.N
bond mol.16.C mol.17.N
bond mol.17.C mol.18.N
bond mol.18.C mol.19.N
savepdb mol ArsD_dry.pdb
saveamberparm mol ArsD_dry.prmtop ArsD_dry.inpcrd
solvatebox mol TIP3PBOX 10.0
addions mol Na+ 0
addions mol Cl- 0
savepdb mol ArsD_solv.pdb
saveamberparm mol ArsD_solv.prmtop ArsD_solv.inpcrd
quit
 
