mdprep input builder

1. Load a structure

Fetch from RCSB

Colab can re-download this by ID, so no file changes hands.

Or upload your own PDB or mmCIF

Stays in this browser. The download at the end bundles it with the manifest so Colab gets the same file.

No structure of your own?

The worked example: an Fe(II)/α-ketoglutarate halogenase with its chloride, its α-ketoglutarate and a water on the iron, fetched from RCSB like any other entry.

Starting the Python runtime…

4. Your mdprep inputs

Manifest

Nothing here is saved anywhere. This page keeps your structure and these answers in the browser only, so download the bundle before you close the tab — it holds the structure and the manifest together, which is what mdprep prepare needs. The manifest does not name a directory on your machine; whoever runs it chooses where the output goes.

Run it in Colab

Open the official mdprep notebook in Colab

Download the bundle above and upload it in section B of the notebook, after section A has installed the programs. The notebook prepares the system, equilibrates it, and lets you look at every step: the structures, the protonation states, the charge on every atom, the metal site, how the box equilibrated, and the MD.

Or paste these two cells into any notebook

mdprep input builder

1. Load a structure

This structure needs a residue renamed

2. What mdprep found

3. Decisions

4. Your mdprep inputs

Manifest

Run it in Colab

Cell 1 — set up the runtime (once per session)

Cell 2 — load the inputs and prepare