GROMACS API

Prepare a solvated molecular-dynamics system from a PDB structure.

Runs the standard pdb2gmx, editconf, and optional solvate preparation steps.

Web form Documentation ↗ Home page ↗ Source code ↗

Submit POST /api/gromacs/

Queues a run and returns 202 with the job.

Schema GET /api/gromacs/

Returns this tool's metadata and the fields below, as JSON.

Request body

Fields

The same names the web form posts. See the field type table for what each kind means over HTTP.

Name	Type	Required	Default	Description
`pdb`	string file	yes	`ATOM 1 N ALA A 1 -0.525 1.363 0.000 1.00 0.00 N ATOM 2 …`	PDB structure Defaults to a minimal alanine example when no file is chosen. file types .pdb,.ent.
`force_field`	string select	no	`amber99sb-ildn`	Force field One of: `amber99sb-ildn`, `charmm27`, `oplsaa`.
`water_model`	string select	no	`tip3p`	Water model One of: `tip3p`, `spce`, `none`.
`box_type`	string select	no	`dodecahedron`	Box type One of: `dodecahedron`, `cubic`, `octahedron`.
`box_distance`	number number	no	`1.0`	Solute-to-box distance (nm) minimum 0.1, maximum 10, step 0.1.
`solvate`	boolean checkbox	no	`true`	Add solvent

Example

A request that runs

These are the defaults, exactly as the web form would post them.

curl -X POST https://www.athanortools.com/api/gromacs/ \
  -H 'Content-Type: application/json' \
  -d '{
  "pdb": "ATOM      1  N   ALA A   1      -0.525   1.363   0.000  1.00  0.00           N\nATOM      2  CA  ALA A   1       0.000   0.000   0.000  1.00  0.00           C\nATOM      3  C   ALA A   1       1.526   0.000   0.000  1.00  0.00           C\nATOM      4  O   ALA A   1       2.153  -1.057   0.000  1.00  0.00           O\nATOM      5  CB  ALA A   1      -0.507  -0.771  -1.216  1.00  0.00           C\nTER\nEND",
  "force_field": "amber99sb-ildn",
  "water_model": "tip3p",
  "box_type": "dodecahedron",
  "box_distance": 1.0,
  "solvate": true
}'

The reply is 202 with a queued job; poll its status_url until status is succeeded or failed. See the quick start for the whole exchange.

Responses

What comes back

status	Meaning
`queued`	Accepted, waiting for the jobs ahead of it. `position` counts how many those are.
`running`	The tool is executing now.
`succeeded`	Finished; `result` holds the tool's output and `license` the terms it came under.
`failed`	Finished; `error` holds a code and a message.

Errors

code	Meaning
`invalid_input`	The client supplied invalid or incomplete input.
`tool_unavailable`	The requested third-party dependency is not available on this host.
`execution_failed`	A configured third-party process exited unsuccessfully.
`internal_error`	An adapter failed in a way it does not describe. The detail is in the server log, not the response.
`not_found`	No job has that id. Finished jobs are dropped eventually.