Description of the error
MDT files can be generated from the 2vb1 CHARMM and the dmpc_in_water NAMD trajectory files from MDANSE-Examples however when you load these MDT files an error occurs.
The following error log is seen with the CHARMM generated MDT files a similar error is seen with NAMD.
Traceback (most recent call last):
File "C:\Users\xcb63893\PycharmProjects\MDANSE\MDANSE\Src\MDANSE\Framework\InputData\HDFTrajectoryInputData.py", line 27, in load
traj = Trajectory(self._name)
^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\xcb63893\PycharmProjects\MDANSE\MDANSE\Src\MDANSE\MolecularDynamics\Trajectory.py", line 71, in __init__
conf = PeriodicRealConfiguration(self._chemical_system, coords, unit_cell)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\xcb63893\PycharmProjects\MDANSE\MDANSE\Src\MDANSE\MolecularDynamics\Configuration.py", line 202, in __init__
super(_PeriodicConfiguration, self).__init__(
File "C:\Users\xcb63893\PycharmProjects\MDANSE\MDANSE\Src\MDANSE\MolecularDynamics\Configuration.py", line 40, in __init__
self["coordinates"] = np.array(coords, dtype=float)
~~~~^^^^^^^^^^^^^^^
File "C:\Users\xcb63893\PycharmProjects\MDANSE\MDANSE\Src\MDANSE\MolecularDynamics\Configuration.py", line 96, in __setitem__
raise ValueError(
ValueError: Invalid item dimensions for coordinates; a shape of (1968, 3) was expected but data with shape of (30714, 3) was provided.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\xcb63893\PycharmProjects\MDANSE\MDANSE_GUI\Src\MDANSE_GUI\Tabs\TrajectoryTab.py", line 47, in load_trajectory
data = HDFTrajectoryInputData(fname[0])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\xcb63893\PycharmProjects\MDANSE\MDANSE\Src\MDANSE\Framework\InputData\InputFileData.py", line 30, in __init__
self.load()
File "C:\Users\xcb63893\PycharmProjects\MDANSE\MDANSE\Src\MDANSE\Framework\InputData\HDFTrajectoryInputData.py", line 31, in load
raise InputDataError(str(e))
MDANSE.Framework.InputData.IInputData.InputDataError: 'Invalid item dimensions for coordinates; a shape of (1968, 3) was expected but data with shape of (30714, 3) was provided.'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\xcb63893\PycharmProjects\MDANSE\MDANSE_GUI\Src\MDANSE_GUI\Tabs\TrajectoryTab.py", line 49, in load_trajectory
self._core.error(repr(e))
TypeError: native Qt signal is not callable
Description of the error MDT files can be generated from the 2vb1 CHARMM and the dmpc_in_water NAMD trajectory files from MDANSE-Examples however when you load these MDT files an error occurs.
The following error log is seen with the CHARMM generated MDT files a similar error is seen with NAMD.