add more review feedback

cookbook/bespoke_parameters_showcase.ipynb

@@ -7,15 +7,17 @@
     "# BespokeFit: Using bespoke force field parameters with OpenFE protocols\n",
     "\n",
     "This tutorial gives a step-by-step guide on the use of OpenFF-BespokeFit generated force field parameters with OpenFE protocols. Here we will focus on relative\n",
-    "binding free energy (RBFE) calculations, but this strategy can be used with any OpenFE protocol. \n",
+    "binding free energy (RBFE) calculations, but this strategy can be used with any OpenMM-based OpenFE protocol. \n",
     "\n",
-    "Here we will assume you have succesfully planned your RBFE campaign using OpenFE by following the [showcase](http://try.openfree.energy/) or [RBFE tutorial](https://docs.openfree.energy/en/stable/tutorials/rbfe_cli_tutorial.html#rbfe-cli-tutorial) and will be using the `TYK2` test system in this example with the planned network provided for you at `assests/ligand_network.graphml`. You should have also already generated a set of bespoke parameters for your ligand series following the [BespokeFit production guide](https://docs.openforcefield.org/projects/bespokefit/en/latest/getting-started/quick-start.html#production-fits) and combined the parameters into a single SMIRNOFF style `offxml` file following the gathering [results guide](https://docs.openforcefield.org/projects/bespokefit/en/latest/users/bespoke-results.html)."
+    "Here we will assume you have succesfully planned your RBFE campaign using OpenFE by following the [showcase](http://try.openfree.energy/) or [RBFE tutorial](https://docs.openfree.energy/en/stable/tutorials/rbfe_cli_tutorial.html#rbfe-cli-tutorial) and will be using the `TYK2` test system in this example with the planned network provided for you at `assests/ligand_network.graphml`. You should have also already generated a set of bespoke parameters for your ligand series following the [BespokeFit production guide](https://docs.openforcefield.org/projects/bespokefit/en/latest/getting-started/quick-start.html#production-fits) and combined the parameters into a single SMIRNOFF style `offxml` file following the [gathering results guide](https://docs.openforcefield.org/projects/bespokefit/en/latest/users/bespoke-results.html)."
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
+    "## Reading input files\n",
+    "\n",
     "Before creating the OpenFE simulation inputs we first we need to load up our planned ligand network of transformations and our bespoke force field file."
    ]
   },
@@ -136,7 +138,7 @@
     "- Store the force field as a string in the OpenFE protocol under the `settings.forcefield_settings.small_molecule_forcefield` field\n",
     "- Use these settings to create the protcol and create the AlchemicalNetwork following the normal steps\n",
     "\n",
-    "Hopefully its clear that this strategy can be applied to any bespoke parameters you wish to add to the force field not just those from BespokeFit, simply edit your base SMIRNOFF style force field using the [OpenFF-Toolkit](https://docs.openforcefield.org/en/latest/examples/openforcefield/openff-toolkit/forcefield_modification/forcefield_modification.html#modifying-a-smirnoff-force-field) set it in the protocol and simulate! \n"
+    "Hopefully its clear that this strategy can be applied to any bespoke parameters you wish to add to the force field not just those from BespokeFit, simply edit your base SMIRNOFF style force field using the [OpenFF-Toolkit](https://docs.openforcefield.org/en/latest/examples/openforcefield/openff-toolkit/forcefield_modification/forcefield_modification.html#modifying-a-smirnoff-force-field), set it in the protocol and simulate! \n"
    ]
   }
  ],