diff --git a/rbfe_tutorial/cli_tutorial.md b/rbfe_tutorial/cli_tutorial.md index e888de9..2275d51 100644 --- a/rbfe_tutorial/cli_tutorial.md +++ b/rbfe_tutorial/cli_tutorial.md @@ -101,6 +101,21 @@ how these simulation are set up: minimum distance of 1.2 nm from the solute to the edge of the box. 4. The protocol used is OpenFE's OpenMM-based Hybrid Topology RFE protocol, with [default settings](https://docs.openfree.energy/en/stable/reference/api/openmm_rfe.html#protocol-settings). +### Customize you Networkplanning with Settings - MORE HERE +You can exchange settings in for the network planning using a `.yaml` file. +```yaml +mapper: + method: kartograf + +network: + method: generate_maximal_network +``` +this you can simply loop in to your CLI command with the `-s` option and a e.g. +`settings.yaml` file: +```bash +openfe plan-rbfe-network -M tyk2_ligands.sdf -p tyk2_protein.pdb -o network_setup -s settings.yaml +``` + ## Running the simulations