From f45973dad04840badd8d612e0d748ecde15f2d13 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 23 Apr 2026 17:45:33 -0700 Subject: [PATCH] adding note about membranes in cli tutorial --- rbfe_tutorial/cli_tutorial.md | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/rbfe_tutorial/cli_tutorial.md b/rbfe_tutorial/cli_tutorial.md index 4c914dc..83ee387 100644 --- a/rbfe_tutorial/cli_tutorial.md +++ b/rbfe_tutorial/cli_tutorial.md @@ -28,8 +28,7 @@ Then when you run `ls`, you should see that your directory has: ## 1. Set up the campaign -The CLI makes setting up the simulation very easy - it's just a single CLI -command. +The CLI makes setting up the simulation very easy - it's just a single CLI command. There are separate commands for relative binding free energy (RBFE) and relative hydration free energy setups (RHFE). For RBFE campaigns, the relevant command is `openfe plan-rbfe-network`. @@ -69,7 +68,13 @@ the number of processors available using the `-n` flag: openfe plan-rbfe-network -M tyk2_ligands.sdf -p tyk2_protein.pdb -o network_setup --n-protocol-repeats 1 -n 4 ``` -This will result in a directory called `network_setup/`, which is structured like this: + +If you are looking to run an RBFE campaign on a system that contains a membrane, you will need to use ``--protein-membrane`` instead of `-p` or ``--protein``. +Membrane-containing protein systems must be provided as fully built, solvated, and pre-equilibrated systems, including correctly defined box vectors. +See the [RBFE calculations of a Protein-Membrane System tutorial](https://docs.openfree.energy/en/latest/tutorials/rbfe_membrane_protein.html) for details on how to prepare the input system. + + +The `openfe plan-rbfe-network` command will result in a directory called `network_setup/`, which is structured like this: