Error running the notebook gromacs/online-tutorials/membrane-protein/main

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question

Error loading notebook

Unreadable Notebook: /home/jovyan/tutorial.ipynb NotJSONError(‘Notebook does not appear to be JSON: '{\n “cells”: [\n {\n “cell_type”: "c…’)

Thanks.

2

Hi,
The cell that produces this issue is the one from line 1513 to 1538:

{
   "cell_type": "code",
   "execution_count": null,
   "id": "34cc9be4-06ca-4418-b9b1-02f43d80a940",
   "metadata": {},
   "outputs": [],
   "source": [
    "import nglview as ng\n",
    "import mdtraj as md\n",
    "trajectory = md.load("step7_production_traj_comp_skip100.xtc", top="step5_input.pdb")\n",
    "view = ng.show_mdtraj(trajectory)\n",
    "view.clear()\n",
    "view.add_cartoon('protein',color_scheme='residueindex')\n",
    "view"
   ]
  },

Just change the md.load call to md.load('step7_production_traj_comp_skip100.xtc', top='step5_input.pdb') (i.e. single quotation marks instad of double).
I have already notified this to the responsable for the tutorials, so hopefully there will be a fix soon.