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tubiana / TTClust

clusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)
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ValueError: xyz must be shape (Any, 2108, 3) I need a help for this #32

Closed hxzwqw closed 2 years ago

hxzwqw commented 2 years ago

Traceback (most recent call last): File "/es01/paratera/sce3820/.conda/envs/sce3820/lib/python3.9/site-packages/mdtraj/core/trajectory.py", line 429, in load t = loader(tmp_file, **kwargs) File "mdtraj/formats/xtc/xtc.pyx", line 168, in mdtraj.formats.xtc.load_xtc File "mdtraj/formats/xtc/xtc.pyx", line 175, in mdtraj.formats.xtc.load_xtc File "mdtraj/formats/xtc/xtc.pyx", line 346, in mdtraj.formats.xtc.XTCTrajectoryFile.read_as_traj File "/es01/paratera/sce3820/.conda/envs/sce3820/lib/python3.9/site-packages/mdtraj/core/trajectory.py", line 1226, in init self.xyz = xyz File "/es01/paratera/sce3820/.conda/envs/sce3820/lib/python3.9/site-packages/mdtraj/core/trajectory.py", line 939, in xyz value = ensure_type(value, np.float32, 3, 'xyz', shape=shape, File "/es01/paratera/sce3820/.conda/envs/sce3820/lib/python3.9/site-packages/mdtraj/utils/validation.py", line 148, in ensure_type raise error ValueError: xyz must be shape (Any, 2108, 3). You supplied (101, 49157, 3)

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/es01/paratera/sce3820/.conda/envs/sce3820/bin/ttclust", line 10, in sys.exit(main()) File "/es01/paratera/sce3820/.conda/envs/sce3820/lib/python3.9/site-packages/ttclust/ttclust.py", line 1329, in main traj = Cluster_analysis_call(args) File "/es01/paratera/sce3820/.conda/envs/sce3820/lib/python3.9/site-packages/ttclust/ttclust.py", line 1229, in Cluster_analysis_call traj = md.load(trajfile, File "/es01/paratera/sce3820/.conda/envs/sce3820/lib/python3.9/site-packages/mdtraj/core/trajectory.py", line 448, in load raise ValueError('The topology and the trajectory files might not contain the same atoms\n' ValueError: The topology and the trajectory files might not contain the same atoms The input topology must contain all atoms even if you want to select a subset of them with atom_indices

tubiana commented 2 years ago

Hi. This error is gaven by MDTRAJ with the clear message : 


The input topology must contain all atoms even if you want to select a subset of them with atom_indices```
This means that your topology and your trajectory don't have the same number of atoms. Maybe you gave the wrong topology or trajectory.