submit_pose_analysis_md_workflow
Run molecular dynamics simulations to analyze protein-ligand binding pose stability, calculate binding free energies, and validate docking results through dynamic simulations.
Instructions
Submit a pose analysis molecular dynamics workflow using Rowan v2 API.
IMPORTANT: The protein parameter must be a UUID (36-character string) of an existing protein in your Rowan account. You cannot use PDB IDs directly. Use the create_protein_from_pdb_id tool first to create a protein, then use its UUID here.
Args: protein: UUID of an existing protein (e.g., "abc123-def456-..."). Get this from create_protein_from_pdb_id or from a previous workflow initial_smiles: SMILES string of the ligand molecule num_trajectories: Number of independent MD simulations to run (default: 1) simulation_time_ns: Simulation time in nanoseconds per trajectory (default: 10ns) ligand_residue_name: Residue name for the ligand in PDB structure (default: "LIG") name: Workflow name for identification and tracking folder_uuid: UUID of folder to organize this workflow. Empty string uses default folder. max_credits: Maximum credits to spend on this calculation. 0 for no limit.
Runs molecular dynamics simulations on protein-ligand complexes to:
Assess binding pose stability over time
Calculate binding free energies
Analyze protein-ligand interactions
Validate docking results with dynamics
Returns: Workflow object representing the submitted workflow
Examples: # Step 1: First create a protein from PDB ID protein_obj = create_protein_from_pdb_id( name="CDK2 Protein", code="1HCK" ) protein_uuid = protein_obj.uuid # Get the UUID
# Step 2: Run MD simulation with the protein UUID
result = submit_pose_analysis_md_workflow(
protein=protein_uuid, # Use the UUID from step 1
initial_smiles="CCC(C)(C)NC1=NCC2(CCC(=O)C2C)N1",
num_trajectories=1,
simulation_time_ns=10,
name="CDK2 Ligand MD"
)
# Or use a protein UUID from list_proteins() output
result = submit_pose_analysis_md_workflow(
protein="550e8400-e29b-41d4-a716-446655440000", # UUID format
initial_smiles="CCO",
num_trajectories=1,
simulation_time_ns=5,
name="Quick MD Validation"
)This workflow can take 1-3 hours depending on simulation length.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| protein | Yes | Protein UUID (36-char string) of existing protein. Use create_protein_from_pdb_id first if needed | |
| initial_smiles | Yes | SMILES string of the ligand molecule | |
| num_trajectories | No | Number of independent MD trajectories to run | |
| simulation_time_ns | No | Simulation time in nanoseconds for each trajectory | |
| ligand_residue_name | No | Residue name for the ligand in the protein structure | LIG |
| name | No | Workflow name for identification and tracking | Pose-Analysis MD Workflow |
| folder_uuid | No | UUID of folder to organize this workflow. Empty string uses default folder | |
| max_credits | No | Maximum credits to spend on this calculation. 0 for no limit |