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Update cookbook/user_charges.ipynb
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IAlibay authored Dec 4, 2023
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"tags": []
},
"source": [
"Components are usually by default loaded into OpenFE without pre-existing partial charges. This is particularly true when loading from [SDF and PDB files](?how do I reference another section?).\n",
"Components are usually by default loaded into OpenFE without pre-existing partial charges. This is particularly true when loading from [SDF and PDB files](https://docs.openfree.energy/en/stable/cookbook/loading_molecules.html).\n",
"\n",
"In those cases, partial charges will be assigned within the selected Protocol. As of writing, for `SmallMoleculeComponent`s this is done using [antechamber's](https://ambermd.org/antechamber/ac.html) `am1bcc` charge assignment, using the input conformer as the pre-optimized input for `sqm`'s AM1 calculation. For `ProteinComponent`s and `SolventComponent`s this is done by assigning charges from the chosen protein and solvent force fields.\n",
"\n",
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