ValueError: attempt to get argmin of an empty sequence for p

With the latest version of YANK, running the p-xylene-implicit example, via:

yank prepare binding amber --setupdir=setup --ligand=“resname BEN” --store=output --iterations=1000 --restraints=harmonic --gbsa=OBC2 --temperature=300*kelvin --verbose

Results in the following error:

Traceback (most recent call last):
  File "/Users/FFF/anaconda/bin/yank", line 9, in <module>
    load_entry_point('yank==0.9.0', 'console_scripts', 'yank')()
  File "/Users/FFF/anaconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-macosx-10.5-x86_64.egg/yank/cli.py", line 105, in main
    dispatched = getattr(commands, command).dispatch(args)
  File "/Users/FFF/anaconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-macosx-10.5-x86_64.egg/yank/commands/prepare.py", line 40, in dispatch
    return dispatch_binding(args)
  File "/Users/FFF/anaconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-macosx-10.5-x86_64.egg/yank/commands/prepare.py", line 254, in dispatch_binding
    utils.config_root_logger(verbose, log_file_path=os.path.join(store_dir, 'prepare.log'))
  File "/Users/FFF/anaconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-macosx-10.5-x86_64.egg/yank/utils.py", line 128, in config_root_logger
    file_handler = logging.FileHandler(log_file_path)
  File "/Users/FFF/anaconda/lib/python2.7/logging/__init__.py", line 905, in __init__
    StreamHandler.__init__(self, self._open())
  File "/Users/FFF/anaconda/lib/python2.7/logging/__init__.py", line 935, in _open
    stream = open(self.baseFilename, self.mode)
IOError: [Errno 2] No such file or directory: '/Users/FFF/anaconda/pkgs/yank/examples/p-xylene-implicit/output/prepare.log'

To get around this, if you mkdir “output” in the same directory, and re-run the above command, the new error becomes:

2016-06-01 00:20:02,601: reading phase complex: 
2016-06-01 00:20:02,602: prmtop: setup/complex.prmtop
2016-06-01 00:20:02,602: inpcrd: setup/complex.inpcrd
2016-06-01 00:20:02,972: reading phase solvent: 
2016-06-01 00:20:02,973: prmtop: setup/solvent.prmtop
2016-06-01 00:20:02,973: inpcrd: setup/solvent.inpcrd
2016-06-01 00:20:03,000: TOTAL ATOMS      :      2621
2016-06-01 00:20:03,000: receptor         :      2621
2016-06-01 00:20:03,000: ligand           :         0
2016-06-01 00:20:03,000: phases: ['complex-implicit', 'solvent-implicit']
2016-06-01 00:20:03,000: systems: ['complex-implicit', 'solvent-implicit']
2016-06-01 00:20:03,001: positions: ['complex-implicit', 'solvent-implicit']
2016-06-01 00:20:03,001: atom_indices: ['complex-implicit', 'solvent-implicit']
2016-06-01 00:20:03,001: thermodynamic_state: <ThermodynamicState object, temperature = 300 K, pressure = 1 atm>
2016-06-01 00:20:03,266: Creating receptor-ligand restraints...
Traceback (most recent call last):
  File "/Users/FFF/anaconda/bin/yank", line 9, in <module>
    load_entry_point('yank==0.9.0', 'console_scripts', 'yank')()
  File "/Users/FFF/anaconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-macosx-10.5-x86_64.egg/yank/cli.py", line 105, in main
    dispatched = getattr(commands, command).dispatch(args)
  File "/Users/FFF/anaconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-macosx-10.5-x86_64.egg/yank/commands/prepare.py", line 40, in dispatch
    return dispatch_binding(args)
  File "/Users/FFF/anaconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-macosx-10.5-x86_64.egg/yank/commands/prepare.py", line 336, in dispatch_binding
    yank.create(phases, systems, positions, atom_indices, thermodynamic_state)
  File "/Users/FFF/anaconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-macosx-10.5-x86_64.egg/yank/yank.py", line 231, in create
    self._create_phase(phase, systems[phase], positions[phase], atom_indices[phase], thermodynamic_state, protocols=protocols)
  File "/Users/FFF/anaconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-macosx-10.5-x86_64.egg/yank/yank.py", line 328, in _create_phase
    restraints = HarmonicReceptorLigandRestraint(thermodynamic_state, reference_system, reference_positions, atom_indices['receptor'], atom_indices['ligand'])
  File "/Users/FFF/anaconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-macosx-10.5-x86_64.egg/yank/restraints.py", line 104, in __init__
    self.restrained_ligand_atom = self._closestAtomToCentroid(self.coordinates, self.ligand_atoms)
  File "/Users/FFF/anaconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-macosx-10.5-x86_64.egg/yank/restraints.py", line 389, in _closestAtomToCentroid
    closest_atom = int(np.argmin(distances))
  File "/Users/FFF/anaconda/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 1028, in argmin
    return argmin(axis, out)

This is run on OSX 10.11.13 using YANK 0.9.0

[jchodera]

We can probably raise an informative exception if the DSL fails to match any atoms

[andrrizzi]

Closing this as it was only an error in the command parameters. The PR #389 adds a more informative error message.