Running a simulation in OpenMM

An error occurred while executing the following cell: ------------------ pdb = mdtraj.load("data/native.pdb") topology = pdb.topology.to_openmm() ------------------ --------------------------------------------------------------------------- OSError Traceback (most recent call last) Cell In[3], line 1 ----> 1 pdb = mdtraj.load("data/native.pdb")  2 topology = pdb.topology.to_openmm() File ~/checkouts/readthedocs.org/user_builds/mdtraj/envs/latest/lib/python3.13/site-packages/mdtraj/core/trajectory.py:435, in load(filename_or_filenames, discard_overlapping_frames, **kwargs)  432 # These topology formats do not support the 'top' keyword  433 # This is to prevent the loader from reading the topology twice.  434 if extension not in [".h5", ".hdf5", ".mol2"]: --> 435 kwargs["top"] = _parse_topology(top, **topkwargs)  437 # get the right loader  438 try: File ~/checkouts/readthedocs.org/user_builds/mdtraj/envs/latest/lib/python3.13/site-packages/mdtraj/core/trajectory.py:195, in _parse_topology(top, **kwargs)  193 match _get_extension(top):  194 case ".pdb" | ".pdb.gz" | ".pdbx" | ".pdbx.gz" | ".cif" | ".cif.gz" | ".mmcif" | ".mmcif.gz": --> 195 _traj = load_frame(top, 0, **kwargs)  196 topology = _traj.topology  197 case ".h5" | ".lh5": File ~/checkouts/readthedocs.org/user_builds/mdtraj/envs/latest/lib/python3.13/site-packages/mdtraj/core/trajectory.py:338, in load_frame(filename, index, top, atom_indices, **kwargs)  336 if not _is_url(filename):  337 if loader.__name__ not in ["load_dtr"]: --> 338 _assert_files_exist(filename)  339 else:  340 _assert_files_or_dirs_exist(filename) File ~/checkouts/readthedocs.org/user_builds/mdtraj/envs/latest/lib/python3.13/site-packages/mdtraj/core/trajectory.py:116, in _assert_files_exist(filenames)  114 for fn in filenames:  115 if not (os.path.exists(fn) and os.path.isfile(fn)): --> 116 raise OSError("No such file: %s" % fn) OSError: No such file: data/native.pdb

(simulation-with-openmm.ipynb; simulation-with-openmm_eval.ipynb; simulation-with-openmm.py)