source leaprc.constph
# Load the PDBs
4lyt = loadPDB 4LYT_Fixed.pdb

# Make the disulfide bonds
bond 4lyt.6.SG 4lyt.127.SG
bond 4lyt.30.SG 4lyt.115.SG
bond 4lyt.64.SG 4lyt.80.SG
bond 4lyt.76.SG 4lyt.94.SG

# Save topology files
saveAmberParm 4lyt 4LYT.parm7 4LYT.rst7

# Quit
quit
