Remove Make.py reference in PyLammps examples

Also fixes some regressions due to command syntax changes

python/examples/pylammps/simple.ipynb

@@ -29,8 +29,7 @@
     "2. Compile LAMMPS as a shared library and enable exceptions and PNG support\n",
     "   ```bash\n",
     "   cd $LAMMPS_DIR/src\n",
-    "   python Make.py -m mpi -png -s exceptions -a file\n",
-    "   make mode=shlib auto\n",
+    "   make mpi mode=shlib LMP_INC=\"-DLAMMPS_PNG -DLAMMPS_EXCEPTIONS\" JPG_LIB=\"-lpng\"\n",
     "   ```\n",
     "\n",
     "3. Create a python virtualenv\n",
@@ -67,7 +66,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "from lammps import IPyLammps"
@@ -144,9 +145,10 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.6.2"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 0
+ "nbformat_minor": 1
 }