source leaprc.constph
source leaprc.conste

# Load PDB
mp8 = loadpdb NAcMP8.constphe.pdb

# Connecting HEH to the protein
bond mp8.14.CB2 mp8.2.CA
bond mp8.14.CB1 mp8.9.CA
bond mp8.14.CBC1 mp8.8.CA
bond mp8.14.CBB2 mp8.5.CA

# Connecting HEH to the PRNs
bond mp8.14.C3D mp8.16.CA
bond mp8.14.C2A mp8.15.CA

# Save topology and coordinate files
saveamberparm mp8 mp8_is.prmtop mp8_is.rst7

# Quit
quit