source leaprc.protein.ff14SB
source leaprc.water.tip3p
loadamberparams frcmod.ionsjc_tip3p
loadamberparams ccl2.frcmod

pep = loadPdb pep1.pdb
ccl2 = loadPdb ccl2.pdb

complex = combine {pep ccl2}
savePdb complex complex1.pdb

solvcomplex = combine {pep ccl2}
solvateBox solvcomplex TIP3PBOX 10

#neutralize the system
addions solvcomplex Cl- 0
addions solvcomplex Na+ 0

savepdb solvcomplex solvcomplex.pdb

#check the system
charge solvcomplex
check solvcomplex
saveAmberParm solvcomplex solvcomplex1.prmtop solvcomplex1.rst7