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cli_tutorials/cli_charge_molecules.md

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# Generating Partial Charges with the OpenFE CLI
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It is recommended to use a single set of charges for each ligand to ensure reproducibility between repeats or consistent
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charges between different legs of a calculation involving the same ligand, like a relative binding affinity calculation for example.
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As such both the `plan-rbfe-network` and `plan-rhfe-network` commands will calculate partial charges for ligands making it expensive
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charges between different legs of a calculation involving the same ligand, like a relative binding affinity calculation for example (see [Osato et al.](https://chemrxiv.org/engage/chemrxiv/article-details/67579833085116a133e39d86)).
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As such both the `plan-rbfe-network` and `plan-rhfe-network` commands will calculate partial charges for ligands making it expensive
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to run multiple network mappings while finding the optimal one for the resources available.
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Here we present a CLI tool to allow you to do this ahead of time, reducing overheads and further improving reproducibility.
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Here we present a CLI tool to do this ahead of time, reducing overheads and further improving reproducibility.
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This tutorial will show you how to use the OpenFE CLI command `charge-molecules` to generate and store partial charges for a series of ligands
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into an SDF file which can be used with OpenFE protocols.
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