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