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fix typo
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jthorton committed Oct 22, 2024
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4 changes: 2 additions & 2 deletions cookbook/bespoke_parameters_showcase.ipynb
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"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 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 `assets/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)."
]
},
{
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"\n",
"# create the solvent and protein components\n",
"solvent = openfe.SolventComponent()\n",
"protein = openfe.ProteinComponent.from_pdb_file(\"assests/tyk2_protein.pdb\")\n",
"protein = openfe.ProteinComponent.from_pdb_file(\"assets/tyk2_protein.pdb\")\n",
"\n",
"# follow the tutorial to create the AlchemicalNetwork\n",
"transformations = []\n",
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