About lab
AutoDock Vina: VinaDockingPredictor Lab
This lab runs a single AutoDock Vina docking job for one prepared receptor and one prepared ligand. Both inputs are PDBQT files. The lab ships with the bundled 1iep complex so a fresh run produces real ranked poses and a structural artifact without any extra setup.
The wrapper boots the pinned official AutoDock Vina 1.2.7 release in managed runtime mode (the binaries are downloaded once and cached), runs classic CPU-backed Vina against the configured search box, and returns ranked poses, an aggregate docking summary, and merged structural files for the top-ranked pose.
This lab is for single-complex docking only. It does not prepare receptors from PDB, prepare ligands from SDF or SMILES, run AutoDock-GPU, or schedule virtual-screening batches. Those belong in adjacent labs.
What You'll See
The lab opens as a small canvas with one Vina docking node and a run-results panel. With the bundled defaults, the run produces:
- a ranked pose table sorted by binding affinity,
- a structure3d view of the top-ranked pose merged onto the receptor,
- a docking summary with run metadata, search box, and Vina stdout/stderr tails.
The first screenshot shows the canvas, node inputs and outputs, and the structure3d view for the top-ranked docked complex. The second scrolls down to the artifact details and ranked pose table for the same run.
How to Read the Visualizations
The pose ranking table lists each Vina pose with its predicted binding affinity (kcal/mol), the lower-bound RMSD to the best pose, and the upper-bound RMSD. Lower (more negative) affinity is a stronger predicted bind. RMSDs near zero for the top entry are normal because Vina ranks against itself. In the screenshot, the bundled 1iep run reports five poses and a top-ranked affinity of -13.314 kcal/mol.
The structure3d view shows the receptor with the highest-affinity pose merged in as top_rank_complex.pdb. Use it to sanity-check that the ligand sits inside the configured search box and inside a plausible pocket. If the ligand sits outside the receptor, the search box is wrong, not the docking. The shown default run places the ligand inside the receptor pocket and exposes the same structure artifact for download.
The docking summary captures the search box, exhaustiveness, scoring function, and the number of poses requested. The run metadata reports which Vina version executed, where the managed runtime cached its binaries, the truncated stdout/stderr from the CLI, and status: ok or status: error so a failed run is still inspectable.
What This Lab Contains
lab.yamldescribes the lab, exposes its inputs and outputs, and pins the bundled defaults.wiring-layout.jsonplaces the model on the canvas.model/model.yamldescribes the model package, parameters, and ports.model/src/vina_docking_predictor.pycontains the wrapper, managed runtime bootstrap, and visualization shaping.model/data/1iep/ships the receptor PDBQT, ligand PDBQT, search-box reference files, and a prepared receptor PDB.model/tests/checks the wrapper, manifest, and lab contract.
Inputs
The model accepts three input signals. Each one falls back to the matching default_* parameter in lab.yaml when the signal is not wired, which is what makes the lab runnable out of the box.
receptor_pdbqt_path(path): prepared receptor PDBQT file. Defaults todata/1iep/1iep_receptor.pdbqt.ligand_pdbqt_path(path): prepared ligand PDBQT file. Defaults todata/1iep/1iep_ligand.pdbqt.run_options(record): Vina CLI options. Defaults to the 1iep-tuned box and exhaustiveness 32.box_center(Å, list of 3): search-box center, in receptor coordinates.box_size(Å, list of 3): search-box edge lengths.exhaustiveness(int): Vina sampling effort. Higher is slower and more thorough.n_poses(int): how many poses to return.energy_range(kcal/mol): max affinity gap from the top pose to keep a pose in the output.cpu(int): CPU thread budget.0lets Vina decide.scoring(str): Vina scoring function (vina,vinardo,ad4).
Outputs
pose_summary(record): ranked poses with affinity, RMSD lower/upper bounds, and per-pose file pointers.docking_summary(record): aggregate stats across the pose set including the search box and Vina settings used.structure_artifacts(record): file-backed artifacts including the mergedtop_rank_complex.pdbconsumed by the structure3d renderer.run_metadata(record): runtime metadata, Vina version, runtime/cache directories, truncated stdout/stderr, andstatus: okorstatus: error.
Running in Biosimulant Desktop
Import the lab once with the Biosim CLI, then open it from the desktop app. The bundled 1iep defaults mean the first run requires no parameter editing.
biosimulant labs import labs/vina-autodock-vina-docking-predictor
To dock a different complex, override the inputs in the lab's run sidebar (or wire them to a source module that produces PDBQT paths). The model treats wired input signals as overrides on top of the defaults, so partial overrides work too.
Notes
- Managed runtime mode is required for remote CPU execution on Modal. System mode (using a pre-installed Vina) is supported for local debugging.
- The lab's
runtime.durationis intentionally short. Vina is event-driven; the wrapper runs the docking job inside a single advance window. - The lab sets
runtime.settle_steps: 1so the downstream visualization module can consume the final structure artifacts without extending simulated time. model/data/1iep/is shipped as part of the model package so the defaults resolve in remote runs too.
Multi-model lab with an embedded visualisation sibling for AutoDock Vina 1.2.7. Ships with the bundled 1iep receptor/ligand PDBQT pair so the lab runs out of the box.
Runtime
Duration0.01
Comms Step0.01
Settle Steps1
Runs
Total2
Completed2
Failed0
Metadata
Packageautodock-vina-vinadockingpredictor-lab
Created2026-05-02
Updated2026-05-15
vinaautodock-vinadockingstructural-biologyprotein-ligandgpuvisualisation
Manifest
{
"io": {
"inputs": [
{
"name": "receptor_pdbqt_path",
"maps_to": "vina_autodock_vina_docking_predictor.receptor_pdbqt_path"
},
{
"name": "ligand_pdbqt_path",
"maps_to": "vina_autodock_vina_docking_predictor.ligand_pdbqt_path"
},
{
"name": "run_options",
"maps_to": "vina_autodock_vina_docking_predictor.run_options"
}
],
"outputs": [
{
"name": "pose_summary",
"maps_to": "vina_autodock_vina_docking_predictor.pose_summary"
},
{
"name": "docking_summary",
"maps_to": "vina_autodock_vina_docking_predictor.docking_summary"
},
{
"name": "structure_artifacts",
"maps_to": "vina_autodock_vina_docking_predictor.structure_artifacts"
},
{
"name": "run_metadata",
"maps_to": "vina_autodock_vina_docking_predictor.run_metadata"
}
]
},
"title": "AutoDock Vina: VinaDockingPredictor Lab",
"models": [
{
"path": "owned/models/vina_autodock_vina_docking_predictor",
"alias": "vina_autodock_vina_docking_predictor",
"parameters": {
"runtime_mode": "managed",
"default_run_options": {
"cpu": 0,
"n_poses": 9,
"scoring": "vina",
"box_size": [
20,
20,
20
],
"box_center": [
15.19,
53.903,
16.917
],
"energy_range": 3,
"exhaustiveness": 32
},
"default_ligand_pdbqt_path": "data/1iep/1iep_ligand.pdbqt",
"default_receptor_pdbqt_path": "data/1iep/1iep_receptor.pdbqt"
},
"provenance": {
"owned_path": "owned/models/vina_autodock_vina_docking_predictor"
}
},
{
"path": "owned/models/visualisation",
"alias": "visualisation",
"parameters": {
"integration_step": 0.01
},
"provenance": {
"owned_path": "owned/models/visualisation"
}
}
],
"wiring": [
{
"to": [
"visualisation.vina_autodock_vina_docking_predictor_pose_summary"
],
"from": "vina_autodock_vina_docking_predictor.pose_summary"
},
{
"to": [
"visualisation.vina_autodock_vina_docking_predictor_docking_summary"
],
"from": "vina_autodock_vina_docking_predictor.docking_summary"
},
{
"to": [
"visualisation.vina_autodock_vina_docking_predictor_structure_artifacts"
],
"from": "vina_autodock_vina_docking_predictor.structure_artifacts"
},
{
"to": [
"visualisation.vina_autodock_vina_docking_predictor_run_metadata"
],
"from": "vina_autodock_vina_docking_predictor.run_metadata"
}
],
"runtime": {
"duration": 0.01,
"settle_steps": 1,
"initial_inputs": {},
"communication_step": 0.01
},
"description": "Multi-model lab with an embedded visualisation sibling for AutoDock Vina 1.2.7. Ships with the bundled 1iep receptor/ligand PDBQT pair so the lab runs out of the box.",
"schema_version": "2.0"
}Sign in to start your own run. Public-lab history stays visible here.
Logs50
2026-05-02 17:43:55 UTCinfosystem
Preparing remote execution...
2026-05-02 17:43:57 UTCinfosystem
Staging package artifacts for remote execution...
2026-05-02 17:44:00 UTCinfosystem
Submitting remote job...
2026-05-02 17:44:03 UTCinfosystem
Running simulation remotely...
2026-05-02 17:44:08 UTCinfosandbox
BSIM_PROGRESS:{"message": "Validating AutoDock Vina inputs", "phase": "inputs"}2026-05-02 17:44:09 UTCinfosandbox
BSIM_PROGRESS:{"message": "Preparing AutoDock Vina runtime", "phase": "runtime"}2026-05-02 17:44:09 UTCinfosandbox
BSIM_PROGRESS:{"message": "Downloading vina_1.2.7_linux_x86_64", "phase": "runtime"}2026-05-02 17:44:10 UTCinfosandbox
BSIM_PROGRESS:{"message": "Downloading vina_split_1.2.7_linux_x86_64", "phase": "runtime"}2026-05-02 17:44:11 UTCinfosandbox
BSIM_PROGRESS:{"message": "Managed AutoDock Vina runtime is ready", "phase": "runtime"}2026-05-02 17:44:11 UTCinfosandbox
BSIM_PROGRESS:{"message": "Writing AutoDock Vina config", "phase": "config"}2026-05-02 17:44:12 UTCinfosandbox
BSIM_PROGRESS:{"message": "Starting AutoDock Vina docking", "phase": "docking"}2026-05-02 17:44:14 UTCinfosystem
Validating AutoDock Vina inputs
2026-05-02 17:44:15 UTCinfosystem
Preparing AutoDock Vina runtime
2026-05-02 17:44:16 UTCinfosystem
Downloading vina_1.2.7_linux_x86_64
2026-05-02 17:44:18 UTCinfosystem
Downloading vina_split_1.2.7_linux_x86_64
2026-05-02 17:44:19 UTCinfosystem
Managed AutoDock Vina runtime is ready
2026-05-02 17:44:20 UTCinfosystem
Writing AutoDock Vina config
2026-05-02 17:44:21 UTCinfosystem
Starting AutoDock Vina docking
2026-05-02 17:44:25 UTCinfosandbox
AutoDock Vina v1.2.7
2026-05-02 17:44:25 UTCinfosandbox
#################################################################
2026-05-02 17:44:26 UTCinfosandbox
# If you used AutoDock Vina in your work, please cite: #
2026-05-02 17:44:27 UTCinfosandbox
# #
2026-05-02 17:44:27 UTCinfosandbox
# J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli #
2026-05-02 17:44:28 UTCinfosandbox
# AutoDock Vina 1.2.0: New Docking Methods, Expanded Force #
2026-05-02 17:44:29 UTCinfosandbox
# Field, and Python Bindings, J. Chem. Inf. Model. (2021) #
2026-05-02 17:44:29 UTCinfosandbox
# DOI 10.1021/acs.jcim.1c00203 #
2026-05-02 17:44:30 UTCinfosandbox
# #
2026-05-02 17:44:31 UTCinfosandbox
# O. Trott, A. J. Olson, #
2026-05-02 17:44:31 UTCinfosandbox
# AutoDock Vina: improving the speed and accuracy of docking #
2026-05-02 17:44:32 UTCinfosandbox
# with a new scoring function, efficient optimization and #
2026-05-02 17:44:33 UTCinfosandbox
# multithreading, J. Comp. Chem. (2010) #
2026-05-02 17:44:33 UTCinfosandbox
# DOI 10.1002/jcc.21334 #
2026-05-02 17:44:34 UTCinfosandbox
# #
2026-05-02 17:44:35 UTCinfosandbox
# Please see https://github.com/ccsb-scripps/AutoDock-Vina for #
2026-05-02 17:44:35 UTCinfosandbox
# more information. #
2026-05-02 17:44:36 UTCinfosandbox
#################################################################
2026-05-02 17:44:36 UTCinfosandbox
Scoring function : vina
2026-05-02 17:44:37 UTCinfosandbox
Rigid receptor: /tmp/biosim-models/vina_autodock_vina_docking_predictor/data/1iep/1iep_receptor.pdbqt
2026-05-02 17:44:38 UTCinfosandbox
Ligand: /tmp/biosim-models/vina_autodock_vina_docking_predictor/data/1iep/1iep_ligand.pdbqt
2026-05-02 17:44:38 UTCinfosandbox
Grid center: X 15.19 Y 53.903 Z 16.917
2026-05-02 17:44:39 UTCinfosandbox
Grid size : X 20 Y 20 Z 20
2026-05-02 17:44:40 UTCinfosandbox
Grid space : 0.375
2026-05-02 17:44:40 UTCinfosandbox
Exhaustiveness: 32
2026-05-02 17:44:41 UTCinfosandbox
CPU: 0
2026-05-02 17:44:42 UTCinfosandbox
Verbosity: 1
2026-05-02 17:44:42 UTCinfosandbox
Computing Vina grid ... done.
2026-05-02 17:44:43 UTCinfosandbox
Performing docking (random seed: 2103551944) ...
2026-05-02 17:44:44 UTCinfosandbox
0% 10 20 30 40 50 60 70 80 90 100%
2026-05-02 17:44:44 UTCinfosandbox
|----|----|----|----|----|----|----|----|----|----|
2026-05-02 17:44:45 UTCinfosandbox
BSIM_PROGRESS:{"duration": 15.0, "message": "AutoDock Vina docking is still running (15s elapsed)", "phase": "docking", "tick": 1}JSON
{
"outputs": {
"vina_autodock_vina_docking_predictor": {
"pose_summary": {
"type": "record",
"source": "vina",
"name": "pose_summary",
"emitted_at": 0.01,
"spec": {
"signal_type": "record",
"kind": "state",
"dtype": null,
"shape": null,
"emitted_unit": null,
"accepted_profiles": null,
"interpolation": "zoh",
"max_age": null,
"stale_policy": "warn",
"schema": {
"payload": "json"
},
"description": null
},
"value": {
"payload": [
{
"rank": 1,
"affinity_kcal_mol": -13.314,
"rmsd_lb": 0,
"rmsd_ub": 0,
"pose_file": "/tmp/bsim-clones/remote-artifacts/cf1eb301-5915-47db-86b4-e80d6ca773d3/vina_autodock_vina_docking_predictor/structure_artifacts/rank_1.pdbqt"
},
{
"rank": 2,
"affinity_kcal_mol": -11.332,
"rmsd_lb": 3.023,
"rmsd_ub": 12.408,
"pose_file": "/tmp/bsim-clones/remote-artifacts/cf1eb301-5915-47db-86b4-e80d6ca773d3/vina_autodock_vina_docking_predictor/structure_artifacts/rank_2.pdbqt"
},
{
"rank": 3,
"affinity_kcal_mol": -11.252,
"rmsd_lb": 1.083,
"rmsd_ub": 1.81,
"pose_file": "/tmp/bsim-clones/remote-artifacts/cf1eb301-5915-47db-86b4-e80d6ca773d3/vina_autodock_vina_docking_predictor/structure_artifacts/rank_3.pdbqt"
},
{
"rank": 4,
"affinity_kcal_mol": -11.171,
"rmsd_lb": 3.807,
"rmsd_ub": 12.278,
"pose_file": "/tmp/bsim-clones/remote-artifacts/cf1eb301-5915-47db-86b4-e80d6ca773d3/vina_autodock_vina_docking_predictor/structure_artifacts/rank_4.pdbqt"
},
{
"rank": 5,
"affinity_kcal_mol": -10.462,
"rmsd_lb": 2.475,
"rmsd_ub": 12.531,
"pose_file": "/tmp/bsim-clones/remote-artifacts/cf1eb301-5915-47db-86b4-e80d6ca773d3/vina_autodock_vina_docking_predictor/structure_artifacts/rank_5.pdbqt"
}
]
}
},
"docking_summary": {
"type": "record",
"source": "vina",
"name": "docking_summary",
"emitted_at": 0.01,
"spec": {
"signal_type": "record",
"kind": "state",
"dtype": null,
"shape": null,
"emitted_unit": null,
"accepted_profiles": null,
"interpolation": "zoh",
"max_age": null,
"stale_policy": "warn",
"schema": {
"payload": "json"
},
"description": null
},
"value": {
"payload": {
"top_pose_rank": 1,
"top_pose_affinity_kcal_mol": -13.314,
"pose_count": 5,
"scoring": "vina",
"exhaustiveness": 32,
"n_poses": 9,
"energy_range": 3,
"cpu": 0,
"seed": 2103551944,
"box_center": [
15.19,
53.903,
16.917
],
"box_size": [
20,
20,
20
]
}
}
},
"structure_artifacts": {
"type": "record",
"source": "vina",
"name": "structure_artifacts",
"emitted_at": 0.01,
"spec": {
"signal_type": "record",
"kind": "state",
"dtype": null,
"shape": null,
"emitted_unit": null,
"accepted_profiles": null,
"interpolation": "zoh",
"max_age": null,
"stale_policy": "warn",
"schema": {
"payload": "json"
},
"description": null
},
"value": {
"payload": {
"output_dir": "/__modal/volumes/vo-ALVkzrP0a5W9UP3ZIorZC4/runtime-work/vina/vina-run-gqjeg748/output",
"docking_output_file": "/tmp/bsim-clones/remote-artifacts/cf1eb301-5915-47db-86b4-e80d6ca773d3/vina_autodock_vina_docking_predictor/structure_artifacts/1iep_ligand_vina_out.pdbqt",
"config_file": "/tmp/bsim-clones/remote-artifacts/cf1eb301-5915-47db-86b4-e80d6ca773d3/vina_autodock_vina_docking_predictor/structure_artifacts/vina.config.txt",
"top_complex_file": "/tmp/bsim-clones/remote-artifacts/cf1eb301-5915-47db-86b4-e80d6ca773d3/vina_autodock_vina_docking_predictor/structure_artifacts/top_rank_complex.pdb",
"pose_summary_file": "/tmp/bsim-clones/remote-artifacts/cf1eb301-5915-47db-86b4-e80d6ca773d3/vina_autodock_vina_docking_predictor/structure_artifacts/pose_summary.json",
"docking_summary_file": "/tmp/bsim-clones/remote-artifacts/cf1eb301-5915-47db-86b4-e80d6ca773d3/vina_autodock_vina_docking_predictor/structure_artifacts/docking_summary.json",
"stdout_tail_file": "/tmp/bsim-clones/remote-artifacts/cf1eb301-5915-47db-86b4-e80d6ca773d3/vina_autodock_vina_docking_predictor/structure_artifacts/stdout_tail.log",
"stderr_tail_file": "/tmp/bsim-clones/remote-artifacts/cf1eb301-5915-47db-86b4-e80d6ca773d3/vina_autodock_vina_docking_predictor/structure_artifacts/stderr_tail.log",
"rank_1_file": "/tmp/bsim-clones/remote-artifacts/cf1eb301-5915-47db-86b4-e80d6ca773d3/vina_autodock_vina_docking_predictor/structure_artifacts/rank_1.pdbqt",
"top_pose_file": "/tmp/bsim-clones/remote-artifacts/cf1eb301-5915-47db-86b4-e80d6ca773d3/vina_autodock_vina_docking_predictor/structure_artifacts/rank_1.pdbqt",
"rank_2_file": "/tmp/bsim-clones/remote-artifacts/cf1eb301-5915-47db-86b4-e80d6ca773d3/vina_autodock_vina_docking_predictor/structure_artifacts/rank_2.pdbqt",
"rank_3_file": "/tmp/bsim-clones/remote-artifacts/cf1eb301-5915-47db-86b4-e80d6ca773d3/vina_autodock_vina_docking_predictor/structure_artifacts/rank_3.pdbqt",
"rank_4_file": "/tmp/bsim-clones/remote-artifacts/cf1eb301-5915-47db-86b4-e80d6ca773d3/vina_autodock_vina_docking_predictor/structure_artifacts/rank_4.pdbqt",
"rank_5_file": "/tmp/bsim-clones/remote-artifacts/cf1eb301-5915-47db-86b4-e80d6ca773d3/vina_autodock_vina_docking_predictor/structure_artifacts/rank_5.pdbqt"
}
}
},
"run_metadata": {
"type": "record",
"source": "vina",
"name": "run_metadata",
"emitted_at": 0.01,
"spec": {
"signal_type": "record",
"kind": "state",
"dtype": null,
"shape": null,
"emitted_unit": null,
"accepted_profiles": null,
"interpolation": "zoh",
"max_age": null,
"stale_policy": "warn",
"schema": {
"payload": "json"
},
"description": null
},
"value": {
"payload": {
"status": "completed",
"runtime_mode": "managed",
"runtime_dir": "/__modal/volumes/vo-ALVkzrP0a5W9UP3ZIorZC4/runtime-cache/vina",
"cache_dir": "/__modal/volumes/vo-ALVkzrP0a5W9UP3ZIorZC4/runtime-cache/vina/downloads",
"vina_version": "1.2.7",
"runtime_bootstrapped": true,
"stdout": "AutoDock Vina v1.2.7\n#################################################################\n# If you used AutoDock Vina in your work, please cite: #\n# #\n# J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli #\n# AutoDock Vina 1.2.0: New Docking Methods, Expanded Force #\n# Field, and Python Bindings, J. Chem. Inf. Model. (2021) #\n# DOI 10.1021/acs.jcim.1c00203 #\n# #\n# O. Trott, A. J. Olson, #\n# AutoDock Vina: improving the speed and accuracy of docking #\n# with a new scoring function, efficient optimization and #\n# multithreading, J. Comp. Chem. (2010) #\n# DOI 10.1002/jcc.21334 #\n# #\n# Please see https://github.com/ccsb-scripps/AutoDock-Vina for #\n# more information. #\n#################################################################\n\nScoring function : vina\nRigid receptor: /tmp/biosim-models/vina_autodock_vina_docking_predictor/data/1iep/1iep_receptor.pdbqt\nLigand: /tmp/biosim-models/vina_autodock_vina_docking_predictor/data/1iep/1iep_ligand.pdbqt\nGrid center: X 15.19 Y 53.903 Z 16.917\nGrid size : X 20 Y 20 Z 20\nGrid space : 0.375\nExhaustiveness: 32\nCPU: 0\nVerbosity: 1\n\nComputing Vina grid ... done.\nPerforming docking (random seed: 2103551944) ... \n0% 10 20 30 40 50 60 70 80 90 100%\n|----|----|----|----|----|----|----|----|----|----|\n***************************************************\n\nmode | affinity | dist from best mode\n | (kcal/mol) | rmsd l.b.| rmsd u.b.\n-----+------------+----------+----------\n 1 -13.31 0 0\n 2 -11.33 3.023 12.41\n 3 -11.25 1.083 1.81\n 4 -11.17 3.807 12.28\n 5 -10.46 2.475 12.53\n 6 -9.915 3.484 12.32\n 7 -9.202 1.629 2.682\n 8 -9.033 3.908 12.69\n 9 -8.866 3.563 12.13\n",
"stderr": "",
"run_root": "/__modal/volumes/vo-ALVkzrP0a5W9UP3ZIorZC4/runtime-work/vina/vina-run-gqjeg748",
"output_dir": "/__modal/volumes/vo-ALVkzrP0a5W9UP3ZIorZC4/runtime-work/vina/vina-run-gqjeg748/output",
"receptor_pdbqt_path": "/tmp/biosim-models/vina_autodock_vina_docking_predictor/data/1iep/1iep_receptor.pdbqt",
"ligand_pdbqt_path": "/tmp/biosim-models/vina_autodock_vina_docking_predictor/data/1iep/1iep_ligand.pdbqt",
"docking_output_path": "/tmp/bsim-clones/remote-artifacts/cf1eb301-5915-47db-86b4-e80d6ca773d3/vina_autodock_vina_docking_predictor/structure_artifacts/1iep_ligand_vina_out.pdbqt",
"config_file": "/tmp/bsim-clones/remote-artifacts/cf1eb301-5915-47db-86b4-e80d6ca773d3/vina_autodock_vina_docking_predictor/structure_artifacts/vina.config.txt",
"resolved_vina_executable": "/__modal/volumes/vo-ALVkzrP0a5W9UP3ZIorZC4/runtime-cache/vina/bin/1.2.7/linux_x86_64/vina",
"resolved_vina_split_executable": "/__modal/volumes/vo-ALVkzrP0a5W9UP3ZIorZC4/runtime-cache/vina/bin/1.2.7/linux_x86_64/vina_split",
"platform_tag": "linux_x86_64",
"command": [
"/__modal/volumes/vo-ALVkzrP0a5W9UP3ZIorZC4/runtime-cache/vina/bin/1.2.7/linux_x86_64/vina",
"--receptor",
"/tmp/biosim-models/vina_autodock_vina_docking_predictor/data/1iep/1iep_receptor.pdbqt",
"--ligand",
"/tmp/biosim-models/vina_autodock_vina_docking_predictor/data/1iep/1iep_ligand.pdbqt",
"--config",
"/tmp/bsim-clones/remote-artifacts/cf1eb301-5915-47db-86b4-e80d6ca773d3/vina_autodock_vina_docking_predictor/structure_artifacts/vina.config.txt",
"--scoring",
"vina",
"--exhaustiveness",
"32",
"--num_modes",
"9",
"--energy_range",
"3.0",
"--cpu",
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"--out",
"/tmp/bsim-clones/remote-artifacts/cf1eb301-5915-47db-86b4-e80d6ca773d3/vina_autodock_vina_docking_predictor/structure_artifacts/1iep_ligand_vina_out.pdbqt"
],
"returncode": 0,
"seed": 2103551944
}
}
}
}
},
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"vina_autodock_vina_docking_predictor": {}
},
"visuals": [
{
"module": "vina_autodock_vina_docking_predictor",
"module_class": "VinaDockingPredictor",
"visuals": [
{
"render": "structure3d",
"data": {
"title": "Top-Ranked Docked Complex",
"source": {
"kind": "artifact",
"artifact_id": "structure-0a87a725c431b229",
"path": "/tmp/bsim-clones/remote-artifacts/cf1eb301-5915-47db-86b4-e80d6ca773d3/vina_autodock_vina_docking_predictor/structure_artifacts/top_rank_complex.pdb"
},
"format": "pdb",
"annotations": [
{
"label": "Top Pose Affinity (kcal/mol)",
"value": -13.314
},
{
"label": "Scoring",
"value": "vina"
},
{
"label": "Pose Count",
"value": 5
}
],
"initial_view": {
"reset_camera": true
}
},
"description": "Top-ranked AutoDock Vina complex for the latest docking run."
},
{
"render": "table",
"data": {
"title": "AutoDock Vina Pose Summary",
"columns": [
"Rank",
"Affinity",
"RMSD l.b.",
"RMSD u.b.",
"Pose File"
],
"rows": [
[
"1",
"-13.314",
"0.0",
"0.0",
"rank_1.pdbqt"
],
[
"2",
"-11.332",
"3.023",
"12.408",
"rank_2.pdbqt"
],
[
"3",
"-11.252",
"1.083",
"1.81",
"rank_3.pdbqt"
],
[
"4",
"-11.171",
"3.807",
"12.278",
"rank_4.pdbqt"
],
[
"5",
"-10.462",
"2.475",
"12.531",
"rank_5.pdbqt"
]
]
},
"description": "Ranked pose summary from the latest AutoDock Vina run."
}
]
}
],
"duration": 0.01,
"communication_step": 0.01,
"modules": [
"vina_autodock_vina_docking_predictor"
],
"lab_commit": "db445aedffb8f0e8c7921f220843a704a87768ce72f7e98008fa9487c9e596d3",
"model_resolutions": [
{
"alias": "vina_autodock_vina_docking_predictor",
"model_id": "embedded:owned/models/vina_autodock_vina_docking_predictor",
"repo_full_name": null,
"commit_sha": null
}
],
"module_ports": {
"vina_autodock_vina_docking_predictor": {
"inputs": [
"ligand_pdbqt_path",
"receptor_pdbqt_path",
"run_options"
],
"outputs": [
"docking_summary",
"pose_summary",
"run_metadata",
"structure_artifacts"
]
}
},
"dependency_installs": [],
"dependency_policy_enabled": true
}