diff --git a/python/converters/vasp/python/inpconf.py b/python/converters/vasp/python/inpconf.py
index 4c91db3f..234a3388 100644
--- a/python/converters/vasp/python/inpconf.py
+++ b/python/converters/vasp/python/inpconf.py
@@ -377,9 +377,10 @@ class ConfigParameters:
                     return ind, shell
             raise KeyError
 
-        sh_inds = []
+        sh_all_inds = []
         for group in self.groups:
             gr_shells = group['shells']
+            sh_inds = []
             for user_ind in gr_shells:
                 try:
                     ind, shell = find_shell_by_user_index(user_ind)
@@ -387,8 +388,9 @@ class ConfigParameters:
                     raise Exception("Shell %i referenced in group '%s' does not exist"%(user_ind, group['index']))
                 sh_inds.append(ind)
 
-# If [Shell] section contains (potentiall conflicting) group parameters
-# remove them and issue a warning
+# If [Shell] section contains (potentially conflicting) group parameters
+# remove them and issue a warning.
+#
 # First, required group parameters
                 for par in self.gr_required.keys():
                     try:
@@ -411,7 +413,11 @@ class ConfigParameters:
                     except KeyError:
                         continue
 
-        sh_refs_used = list(set(sh_inds))
+            sh_all_inds += sh_inds
+# Replace user shell indices with internal ones
+            group['shells'] = sh_inds
+
+        sh_refs_used = list(set(sh_all_inds))
         sh_refs_used.sort()
 
 # Check that all shells are referenced in the groups
@@ -432,8 +438,7 @@ class ConfigParameters:
 
 ################################################################################
 #
-# Main parser
-# parse_logical()
+# Main parser function
 #
 ################################################################################
     def parse_input(self):
diff --git a/python/converters/vasp/test/inpconf/test_inpconf.py b/python/converters/vasp/test/inpconf/test_inpconf.py
index 08bfa243..7a893cb1 100644
--- a/python/converters/vasp/test/inpconf/test_inpconf.py
+++ b/python/converters/vasp/test/inpconf/test_inpconf.py
@@ -298,6 +298,8 @@ class TestSpecialParsers(unittest.TestCase):
           **raise** Exception
         - **if** not all defined shells are referenced in the groups
           **raise** Exception
+        - **if** all sections are parsed error-free check that the output
+          is correct
         """
 # Scenario 1
         conf_pars = ConfigParameters('test6.cfg')
@@ -323,6 +325,28 @@ class TestSpecialParsers(unittest.TestCase):
         with self.assertRaisesRegexp(AssertionError, err_mess):
             conf_pars.parse_input()
 
+# Scenario 5
+        conf_pars = ConfigParameters('test7.cfg')
+        conf_pars.parse_input()
+#        with open('parse_input.output.test', 'wt') as f:
+#            f.write("Shells:\n")
+#            f.write(conf_pars.shells.__repr__() + '\n\n')
+#            f.write("Groups:\n")
+#            f.write(conf_pars.groups.__repr__() + '\n')
+        res = "Shells:\n"
+        res += conf_pars.shells.__repr__() + '\n\n'
+        res += "Groups:\n"
+        res += conf_pars.groups.__repr__()
+
+        expected = r"""Shells:
+[{'ion_list': array([4, 5, 6, 7]), 'user_index': 1, 'lshell': 2}, {'tmatrix': array([[ 0.,  1.,  0.],
+       [ 1.,  0.,  0.],
+       [ 0.,  0.,  1.]]), 'ion_list': array([0, 1, 2, 3]), 'user_index': 2, 'lshell': 1}, {'ion_list': array([0, 1, 2, 3]), 'user_index': 3, 'lshell': 3}]
+
+Groups:
+[{'index': 1, 'shells': [0, 1], 'emin': -7.6, 'emax': 3.0}, {'index': 2, 'shells': [2], 'emin': -1.6, 'emax': 2.0}]"""
+
+        self.assertEqual(res, expected)