atom delete

You can use the delete atoms command without the porosity style. If you know the atoms (the type of atoms) you want to delete you can group them and use the delete_atoms command.

If the atoms are a part of bond, angle, dihedral you may want to delete those topological interactions before deleting the atom
by using "delete bonds " command so that it does not leave a dangling bond. Also use the “special” keyword to update the scaled pair wise interaction weighting coefficients.