Answer only the questions your structure needs, then take the manifest
to Colab. Your structure is read in your browser and never uploaded.
1. Load a structure
Colab can re-download this by ID, so no file changes hands.
Stays in this browser. The download at the end bundles it with the
manifest so Colab gets the same file.
Starting the Python runtime…
This structure needs a residue renamed
Or rename it yourself in the input file and load it again. Nothing is
prepared until the name is changed.
2. What mdprep found
3. Decisions
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.
Download the bundle above and upload it in section B of the notebook.
It installs exactly what this manifest needs, 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.