source leaprc.gaff2
source leaprc.protein.ff14SB
source leaprc.water.tip3p
loadOff atomic_ions.lib
loadOff solvents.lib
parm10 = loadamberparams parm10.dat
frcmod14SB = loadamberparams frcmod.ff14SB
loadamberprep acetonitrile.prepi
loadamberparams acetonitrile.frcmod
pro=loadpdb setup_ABL_Kinase_transformed.pdb
solvatebox pro TIP3PBOX 10
charge pro
addions pro Na+ 0
savepdb pro pro_WAT_box.pdb
saveamberparm pro pro_WAT.prmtop pro_WAT.inpcrd
