loadRestrt solv.rst7
setOverwrite True
# First reset all of the molecules in the system, but count the ions
# as part of the bulk solvent rather than as part of the solute.
setMolecules solute_ions False
outparm ions_solvent.parm7

# Now combine the first 2 molecules, since it's a protein-ligand system. This
# will prevent the complex from imaging separately.
combineMolecules 1 2
outparm CM_Solvent_ions.parm7

# Now re-set the molecules, treating the ions as part of the solute again, but
# re-combine the first 2 molecules
setMolecules True
combineMolecules 1 2
outparm CM_Solute_ions.parm7

# Now remove the solvent and ions and change pbradii to mbondi3 for igb=8
# mm/gbsa
strip :WAT,Cl-
changeRadii mbondi3
outparm CM_stripped.parm7 CM_stripped.rst7