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)  in  ----> 1 pdb = mdtraj.load('data/native.pdb')  2 topology = pdb.topology.to_openmm() ~/miniconda3/envs/docenv/lib/python3.6/site-packages/mdtraj/core/trajectory.py in load(filename_or_filenames, discard_overlapping_frames, **kwargs)  424   425 if loader.__name__ not in ['load_dtr']: --> 426 _assert_files_exist(filename_or_filenames)  427 else:  428 _assert_files_or_dirs_exist(filename_or_filenames) ~/miniconda3/envs/docenv/lib/python3.6/site-packages/mdtraj/core/trajectory.py in _assert_files_exist(filenames)  97 for fn in filenames:  98 if not (os.path.exists(fn) and os.path.isfile(fn)): ---> 99 raise IOError('No such file: %s' % fn)  100   101  OSError: No such file: data/native.pdb OSError: No such file: data/native.pdb

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