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Prerequisites:
  • A registered Asclepius account
  • A generated API key associated with the account
Follow these steps to install and run Mintlify on your operating system.
1

Request a secure upload URL

curl --request GET \
  --url 'https://98i2es6mi4.execute-api.us-west-2.amazonaws.com/prod/submit/upload-url?filetype=pdb' \
  --header 'x-api-key: <api-key>'
2

Upload your custom simulation files

Copy the secure upload link obtained in the previous step and run the following command:
curl --upload-file ./myfile.pdb \
     -H "Content-Type: chemical/x-pdb" \
     "https://your-presigned-url..."
A 3d render of your molecules and preview of your files will be available through the Asclepius UI.
3

Register your new files

curl --request POST \
  --url https://98i2es6mi4.execute-api.us-west-2.amazonaws.com/prod/submit/file/ \
  --header 'Content-Type: application/json' \
  --header 'x-api-key: <api-key>' \
  --data '{
  "name": "<string>",
  "type": "<string>",
  "format": "<string>",
  "file_id": "<string>"
}'
A 3d render of your molecules and preview of your files will be available through the Asclepius UI.
4

Build a system

Gather your system requirements including force fields, molecules, and environment before running the next command to build your system.
curl --request POST \
  --url https://98i2es6mi4.execute-api.us-west-2.amazonaws.com/prod/submit/system \
  --header 'Content-Type: application/json' \
  --header 'x-api-key: <api-key>' \
  --data '{
  "box_name": "<string>",
  "box_shape": "<string>",
  "chain_id": "<string>",
  "concentration": 123,
  "force_field": "<string>",
  "ions": "<string>",
  "keep_Hs": true,
  "ligand_input_formats": [
    "<string>"
  ],
  "ligand_residue_names": [
    "<string>"
  ],
  "ligand_rotations": [
    [
      "<any>"
    ]
  ],
  "ligand_translations": [
    [
      "<any>"
    ]
  ],
  "ligands": [
    "<string>"
  ],
  "membrane": "<string>",
  "minimum_padding": 123,
  "pH": 123,
  "protein": "<string>",
  "water_type": "<string>"
}'
5

Submit a simulation

Copy the secure upload link obtained in the previous step and run the following command:
curl --request POST \
  --url https://98i2es6mi4.execute-api.us-west-2.amazonaws.com/prod/submit/job \
  --header 'Content-Type: application/json' \
  --header 'x-api-key: <api-key>' \
  --data '{
  "batch_index": 1,
  "batch_name": "<string>",
  "equilibration": [
    {
      "traj_freq": 1,
      "time": 1,
      "log_freq": 1,
      "type": "<string>",
      "restraint_force": 1,
      "restraint_mask": "<string>"
    }
  ],
  "production": {
    "traj_freq": 1,
    "time": 1,
    "log_freq": 1,
    "type": "<string>"
  },
  "temperature": 1,
  "pressure": 1,
  "surface_tension": 1,
  "friction": 1,
  "integration_timestep": 1,
  "ewald_error_tolerance": 1,
  "non_bonded_cutoff": 1,
  "minimization_steps": 1,
  "trajectory_output_format": "<string>"
}'
6

Analyze your trajectory

To run your own analysis on the trajectory that was calculated, run the following command:
curl --request POST \
  --url https://98i2es6mi4.execute-api.us-west-2.amazonaws.com/prod/submit/analysis \
  --header 'Content-Type: application/json' \
  --header 'x-api-key: <api-key>' \
  --data '{
  "downsample_frames": 123,
  "distance_masks": [
    "<string>"
  ],
  "rmsd_masks": [
    [
      "<string>"
    ]
  ],
  "rmsf_masks": [
    "<string>"
  ],
  "hbond_angle": 123,
  "hbond_distance": 123
}'
7

Download results

curl --request GET \
  --url https://98i2es6mi4.execute-api.us-west-2.amazonaws.com/prod/retrieve/job/{job_id} \
  --header 'x-api-key: <api-key>'