Remove redundant PROPKA script.

Fixes https://github.com/jensengroup/propka-3.1/pull/61#discussion_r442401079

scripts/propka3.py

@@ -1,36 +0,0 @@
-#!/usr/bin/env python
-"""PROPKA script.
-
-This is the original propka script. However, this distribute-based
-installation moved the main() function into propka.run.main and just
-generates a script called `propka3` from the setup.py installation
-script. You should not need to use this script.
-
-(Also note that there can be import problems because the script name
-is the same as the module name; that's why the new script is called
-`propka3`.)
-"""
-from propka.lib import loadOptions
-from propka.input import read_parameter_file, read_molecule_file
-from propka.parameters import Parameters
-from propka.molecular_container import MolecularContainer
-
-
-def main():
-    """Read in structure files, calculates pKa values, and prints pKa files."""
-    # loading options, flaggs and arguments
-    options = loadOptions([])
-    pdbfiles = options.filenames
-    parameters = read_parameter_file(options.parameters, Parameters())
-
-    for pdbfile in pdbfiles:
-        my_molecule = MolecularContainer(parameters, options)
-        my_molecule = read_molecule_file(pdbfile, my_molecule)
-        my_molecule.calculate_pka()
-        my_molecule.write_pka()
-        if options.generate_propka_input:
-            my_molecule.write_propka()
-
-
-if __name__ == '__main__':
-    main()