> ## Documentation Index > Fetch the complete documentation index at: https://docs.revilico.bio/llms.txt > Use this file to discover all available pages before exploring further. # Start a RevFEP run > Ranks a series of related drug-like molecules by how strongly each binds a protein, by simulating the change from one molecule into another (relative binding free energy, OpenFE). Gives the difference in binding free energy (kcal/mol) for every planned pair of molecules and a relative value per molecule. Slow and accurate: hours of GPU time per pair. The inputs are checked before the run starts. Runs cannot be cancelled once submitted. Starts a run and returns it with status `queued`; poll GET /v1/runs/{runId} until it finishes. Runs spend credits. **Limits:** `minLigands`: 2, `maxLigands`: 201, `maxLigandHeavyAtoms`: 200, `maxEstimatedGpuHours`: 2000. How the engine works and how to read its results: [RevFEP documentation](/docs/revfep). **Scope:** `runs:write`. ## OpenAPI ````yaml /api-reference/openapi.json post /v1/engines/revfep/runs openapi: 3.1.0 info: title: Revilico API version: 1.0.0 description: >- Run Revilico's computational chemistry and biology engines from your own code: upload input files, start runs, follow them and read their results. servers: - url: https://public-api.revilico.bio security: - bearerAuth: [] tags: - name: Account description: Who you are, your credits and what your runs have used. - name: Engines description: The engines you can run, their parameter schemas and examples. - name: Files description: 'Upload input files: create an upload, then PUT the bytes.' - name: Runs description: Start, follow and cancel engine runs. - name: Results and outputs description: 'Read what a run produced: results, files and outputs.' - name: Projects description: Group runs into the projects you see in the web app. - name: Sharing description: >- Share runs with people in your organization, as in the web app's Pipeline sharing. - name: Notes description: >- RevNotes: read, write and share the rich-text notes and note folders of the web app's RevNotes panel, in markdown or HTML. - name: Drive description: >- Your RevDrive files and shared drives, as in the web app: browse, read, use files as run inputs, save outputs, and organize. Ids: `dfile_…` and `dfld_…` in a personal Drive, `drive_…` for a shared drive, `sdfile_…` and `sdfld_…` in one. - name: Engine runs description: >- Start a run of one engine, with that engine's parameters and input files. Same endpoint as **Start a run**. - name: Health description: Service status. Needs no API key. paths: /v1/engines/revfep/runs: post: tags: - Engine runs summary: Start a RevFEP run description: >- Ranks a series of related drug-like molecules by how strongly each binds a protein, by simulating the change from one molecule into another (relative binding free energy, OpenFE). Gives the difference in binding free energy (kcal/mol) for every planned pair of molecules and a relative value per molecule. Slow and accurate: hours of GPU time per pair. The inputs are checked before the run starts. Runs cannot be cancelled once submitted. Starts a run and returns it with status `queued`; poll GET /v1/runs/{runId} until it finishes. Runs spend credits. **Limits:** `minLigands`: 2, `maxLigands`: 201, `maxLigandHeavyAtoms`: 200, `maxEstimatedGpuHours`: 2000. How the engine works and how to read its results: [RevFEP documentation](/docs/revfep). **Scope:** `runs:write`. operationId: engineRuns.revfep requestBody: required: true content: application/json: schema: type: object properties: name: description: A name for the run, shown in the web app. type: string maxLength: 200 parameters: type: object properties: protocol: default: rbfe description: >- rbfe: relative binding free energy, the difference in binding strength between pairs of similar ligands. The only protocol available today. type: string enum: - rbfe preset: default: validated description: >- Starting values for the simulation settings below; any of them can still be set. validated: the protocol checked against published benchmarks (5 ns per window, 1 repeat). minimum: a quick test that the inputs run (2 ns, no replica exchange); its numbers are rough. production: validated with 3 repeats, so each result has an error estimate. high: 10 ns, 21 windows, 5 repeats; the most accurate and about 20 times the GPU time of validated. type: string enum: - validated - minimum - production - high charge_method: description: >- How partial charges are assigned to ligand atoms. am1bcc (default) is the standard; am1bccelf10 averages over conformers and is slower; espaloma uses a machine-learned model. type: string enum: - am1bcc - am1bccelf10 - espaloma small_molecule_force_field: description: >- Force field (the physics model) for the ligands. openff-2.2.0 (default) is the one the validated protocol uses. type: string enum: - openff-2.2.0 - openff-2.0.0 - openff-2.1.0 - openff-1.3.1 - gaff-2.11 production_length_ns: description: >- Simulated time per window and leg, in nanoseconds (preset default: 5, or 2 for minimum, 10 for high). Longer gives more converged results; GPU time grows in proportion. type: number minimum: 0.1 maximum: 100 equilibration_length_ns: description: >- Settling time before measurement starts, per window, in nanoseconds (preset default: 1, or 0.5 for minimum, 2 for high). type: number minimum: 0.05 maximum: 10 protocol_repeats: description: >- Independent repeats of every calculation (preset default: 1, or 3 for production, 5 for high). With 2 or more, each result gets an error estimate; GPU time grows in proportion. type: integer minimum: 1 maximum: 10 lambda_windows: description: >- Intermediate steps between the two ligands of a pair (preset default: 11, or 21 for high). More windows help pairs that differ a lot; GPU time grows in proportion. The engine needs at least 11. type: integer minimum: 11 maximum: 64 sampler: description: >- repex (replica exchange, the default) lets neighbouring windows swap states, which converges faster; independent runs each window on its own (the minimum preset). type: string enum: - repex - independent minimization_steps: description: >- Energy-minimisation steps before each simulation starts (default 10000). type: integer minimum: 500 maximum: 100000 solvent_padding_nm: description: >- Minimum water layer around the protein and ligand, in nanometres (preset default: 1.5, or 1.2 for the other presets). A larger box is slower. type: number minimum: 1 maximum: 3 ion_concentration_m: description: >- Salt concentration of the water, in mol/L (default 0.15). type: number minimum: 0 maximum: 1 hydrogen_mass_repartitioning: description: >- Make hydrogen atoms heavier so the simulation can take longer time steps. Off by default: it is faster but can make free-energy results drift. type: boolean atom_mapper: description: >- How atoms of one ligand are matched to the other in each pair. lomap (default, validated) matches by shared substructure; kartograf matches by 3D position, so the ligands must be posed consistently. type: string enum: - lomap - kartograf network: description: >- Which pairs are computed. mst (default) links every ligand with the fewest, most similar pairs; lomap adds redundant pairs that form closed loops, which cross-check each other at extra GPU cost. type: string enum: - mst - lomap allow_element_change: description: >- Allow matched atoms to change element (for example Cl to H, C to N). On by default; off makes the matched part of each pair smaller. type: boolean kartograf_max_distance_angstrom: description: >- kartograf only: how far apart, in ångström, two atoms may be and still be matched (default 0.95). type: number minimum: 0.1 maximum: 5 kartograf_exact_rings: description: >- kartograf only: match ring atoms only when whole rings match (default true). type: boolean additionalProperties: false inputs: type: object properties: protein: type: string description: >- The target protein (PDB), prepared for simulation: hydrogens added, missing loops and side chains filled in, only the chains, waters and ions you want kept. The ligands must sit in its binding site. A file id: an upload (`file_…`) or a Drive file (`dfile_…`, `sdfile_…`). Formats: pdb; up to 50 MB. ligands: type: string description: >- The ligand series (V2000 SDF): 2 to 201 related molecules with hydrogens, each posed in the binding site in 3D (aligned on a shared core), with a unique name on the first line of its record, the same net charge and at most 200 heavy atoms. An experimental value per ligand (an SD tag such as exp_dg in kcal/mol, or IC50/Ki in nM) is compared with the predictions when present. A file id: an upload (`file_…`) or a Drive file (`dfile_…`, `sdfile_…`). Formats: sdf; up to 50 MB. required: - protein - ligands additionalProperties: false budget: description: Most credits the run may spend; it is stopped beyond that. type: number exclusiveMinimum: 0 projectId: description: >- Add the run to this project (`proj_…`); needs editor or owner on it. type: string required: - inputs additionalProperties: false examples: validated: summary: >- Rank a congeneric series against one protein with the validated protocol: one free-energy difference per pair of ligands. value: name: CDK2 series A parameters: {} inputs: protein: file_… ligands: file_… production-with-errors: summary: >- Three repeats of every calculation, so each pair gets an error estimate, with extra pairs that cross-check each other. value: name: CDK2 series A, 3 repeats parameters: preset: production network: lomap inputs: protein: file_… ligands: file_… quick-check: summary: >- A short, cheap run to check that the protein and ligands go through every stage before paying for a real one. value: parameters: preset: minimum inputs: protein: file_… ligands: file_… responses: '202': description: OK content: application/json: schema: $ref: '#/components/schemas/Run' '400': $ref: '#/components/responses/400' '401': $ref: '#/components/responses/401' '402': $ref: '#/components/responses/402' '403': $ref: '#/components/responses/403' '404': $ref: '#/components/responses/404' '422': $ref: '#/components/responses/422' '500': $ref: '#/components/responses/500' '502': $ref: '#/components/responses/502' components: schemas: Run: type: object properties: id: type: string description: Run id, `run_…`. engine: type: string description: Engine slug, e.g. `revredox`. name: type: - string - 'null' access: type: string enum: - owner - shared - project description: >- Why you can see the run: you started it, it was shared with you, or it is in a project you belong to. Only the owner can cancel it or read its inputs. owner: type: object properties: name: type: - string - 'null' email: type: string required: - name - email description: Who started the run. status: type: string enum: - queued - running - succeeded - failed - cancelled description: >- queued until the engine picks the run up; succeeded, failed and cancelled are final. statusReason: description: >- Why a cancelled run stopped: `user`, `insufficient_credits` or `budget_exceeded`. Null otherwise. type: - string - 'null' progress: type: number description: Progress the engine reports; 0 until it reports any. createdAt: type: string format: date-time startedAt: anyOf: - type: string format: date-time - type: 'null' endedAt: anyOf: - type: string format: date-time - type: 'null' budget: description: Most credits the run may spend, if one was set. type: - number - 'null' creditsUsed: type: number description: Credits charged to the run so far. error: anyOf: - type: object properties: message: type: string required: - message - type: 'null' description: Set when status is failed. children: type: object properties: total: type: number queued: type: number running: type: number succeeded: type: number failed: type: number cancelled: type: number required: - total - queued - running - succeeded - failed - cancelled description: >- For engines that run each input as its own job: how many children are in each status. GET /v1/runs/{runId}/children lists them. links: type: object propertyNames: type: string additionalProperties: type: string description: >- Related endpoints: self, inputs (owner only), results, outputs, files. warnings: description: >- Set when the run was created but a follow-up step, such as adding it to a project, failed. type: array items: type: string required: - id - engine - name - access - owner - status - statusReason - progress - createdAt - startedAt - endedAt - budget - creditsUsed - error - links Error: type: object properties: error: type: object properties: code: type: string enum: - VALIDATION_FAILED - INVALID_ID - INVALID_PARAMETERS - INPUT_LIMIT_EXCEEDED - NOT_FOUND - FORBIDDEN - METHOD_NOT_ALLOWED - CONFLICT - PAYLOAD_TOO_LARGE - MISSING_CREDENTIALS - INVALID_CREDENTIALS - WRONG_ENVIRONMENT - CREDENTIALS_EXPIRED - CREDENTIALS_REVOKED - ACCOUNT_INACTIVE - API_ACCESS_NOT_ENABLED - INSUFFICIENT_SCOPE - SESSION_REQUIRED - TOO_MANY_AUTH_FAILURES - API_KEY_LIMIT_REACHED - ENGINE_NOT_ENABLED - DOCS_NOT_AVAILABLE - INSUFFICIENT_CREDITS - RUN_NOT_COMPLETE - ENGINE_SUBMIT_FAILED - RATE_LIMITED - SERVICE_UNAVAILABLE - INTERNAL_ERROR description: Stable within /v1; branch on this, not on the message. message: type: string description: Readable explanation, for people. details: description: >- Extra context, e.g. `issues` ({ path, message }[]) for validation errors. type: object propertyNames: type: string additionalProperties: {} required: - code - message required: - error responses: '400': description: >- The request is malformed. `error.code` is one of `VALIDATION_FAILED`, `INVALID_ID`. content: application/json: schema: $ref: '#/components/schemas/Error' example: error: code: VALIDATION_FAILED message: The request is malformed. '401': description: >- The API key is missing or not valid. `error.code` is one of `MISSING_CREDENTIALS`, `INVALID_CREDENTIALS`, `WRONG_ENVIRONMENT`, `CREDENTIALS_EXPIRED`, `CREDENTIALS_REVOKED`. content: application/json: schema: $ref: '#/components/schemas/Error' example: error: code: MISSING_CREDENTIALS message: The API key is missing or not valid. '402': description: >- Your organization doesn't have enough credits. `error.code` is one of `INSUFFICIENT_CREDITS`. content: application/json: schema: $ref: '#/components/schemas/Error' example: error: code: INSUFFICIENT_CREDITS message: Your organization doesn't have enough credits. '403': description: >- The key may not do this. `error.code` is one of `INSUFFICIENT_SCOPE`, `API_ACCESS_NOT_ENABLED`, `ENGINE_NOT_ENABLED`, `ACCOUNT_INACTIVE`, `FORBIDDEN`. content: application/json: schema: $ref: '#/components/schemas/Error' example: error: code: INSUFFICIENT_SCOPE message: The key may not do this. '404': description: Not found, or not visible to you. `error.code` is one of `NOT_FOUND`. content: application/json: schema: $ref: '#/components/schemas/Error' example: error: code: NOT_FOUND message: Not found, or not visible to you. '422': description: >- The parameters or input files don't fit the engine. `error.code` is one of `INVALID_PARAMETERS`, `INPUT_LIMIT_EXCEEDED`. content: application/json: schema: $ref: '#/components/schemas/Error' example: error: code: INVALID_PARAMETERS message: The parameters or input files don't fit the engine. '500': description: >- Something went wrong on our side. `error.code` is one of `INTERNAL_ERROR`. content: application/json: schema: $ref: '#/components/schemas/Error' example: error: code: INTERNAL_ERROR message: Something went wrong on our side. '502': description: >- The engine service rejected or failed the request. `error.code` is one of `ENGINE_SUBMIT_FAILED`. content: application/json: schema: $ref: '#/components/schemas/Error' example: error: code: ENGINE_SUBMIT_FAILED message: The engine service rejected or failed the request. securitySchemes: bearerAuth: type: http scheme: bearer description: >- An API key from the web app (**Settings → Developer**), sent as `Authorization: Bearer rvl_live_…`. ```` This documentation is built and hosted on [Mintlify](https://mintlify.com), a developer documentation platform.