Modify simulateCharmm.py to require a top and par file. Delete charmm22 files

to prevent users from actually using them.

examples/simulateCharmm.py

 from simtk.openmm.app import *
 from simtk.openmm import *
 from simtk.unit import *
-from sys import stdout
+from sys import stdout, exit, stderr
+
+# Define a user-interface
+from optparse import OptionParser
+
+parser = OptionParser()
+parser.add_option('-t', '--top', dest='top', default=None,
+                  help='CHARMM RTF file to use in the simulation.')
+parser.add_option('-p', '--param', dest='par', default=None,
+                  help='CHARMM parameter file to use in the simulation.')
+opt, arg = parser.parse_args()
+
+if arg:
+    stderr.write('Unexpected arguments: %s' % ', '.join(arg) + '\n')
+    exit(parser.print_help() or 1)
+if opt.top is None or opt.par is None:
+    stderr.write('You must provide a top AND parameter file\n')
+    exit(parser.print_help() or 1)
 
 # Read the PSF
 psf = CharmmPsfFile('ala_ala_ala.psf')
@@ -10,7 +27,7 @@ psf = CharmmPsfFile('ala_ala_ala.psf')
 pdb = PDBFile('ala_ala_ala.pdb')
 
 # Read and condense the parameter set
-params = CharmmParameterSet('charmm22.rtf', 'charmm22.par')
+params = CharmmParameterSet(opt.top, opt.par)
 
 # Instantiate the system
 system = psf.createSystem(params, nonbondedMethod=NoCutoff,