Use charged ligands across all tutorials except charging tutorials

ahfe_tutorial/ahfe_tutorial.ipynb

@@ -111,10 +111,22 @@
    "outputs": [],
    "source": [
     "from rdkit import Chem\n",
-    "supp = Chem.SDMolSupplier(\"../cookbook/assets/benzene.sdf\", removeHs=False)\n",
+    "supp = Chem.SDMolSupplier(\"../cookbook/assets/benzene_am1bcc.sdf\", removeHs=False)\n",
     "ligands = [openfe.SmallMoleculeComponent.from_rdkit(mol) for mol in supp]"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "e3ee0b9c-4221-4953-8ceb-f84f821a4388",
+   "metadata": {},
+   "source": [
+    "<div class=\"alert alert-block alert-info\">\n",
+    "\n",
+    "**Partial charges:** The ligand in `benzene_am1bcc.sdf` already has AM1-BCC partial charges, so the same charges are used in every repeat. To assign partial charges to your own ligands, see the cookbook on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/cookbook/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
+    "\n",
+    "</div>"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "d0cb1329",
@@ -1038,7 +1050,7 @@
     "# }\n",
     "\n",
     "# with open(\"ahfe_json/benzene_results.json\") as stream:\n",
-    "#     json.dump(outdict, stream, cls=gufe.tokenization.JSON_HANDLER.encoder)"
+    "#     json.to_json(outdict, stream, cls=gufe.tokenization.JSON_HANDLER.encoder)"
    ]
   },
   {
@@ -1116,7 +1128,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.14.7"
+   "version": "3.13.14"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {