Closed sryckbos closed 10 years ago
Yeah, for sure. That is a somewhat "obvious" error mode (using files that don't mesh with one another) that we should definitely check for explicitly and give a nice error message with. Can you post the full traceback that the error came from, so I can flag the line number?
Sure, here you go!
Traceback (most recent call last):
File "/home/sryckbos/epd-7.3-2-rh5-x86_64/bin/ConvertDataToHDF.py", line 216, in
I think this is fixed in the master version? Do you know what version of msmbuilder you're using? On the master branch, I get this error when I use an incorrect pdb in ConvertDataToHDF.py
$ ConvertDataToHDF.py -i ~/local/msmbuilder/Tutorial/XTC -s ~/projects/met-enkephalin/1PLX-0-solvated.pdb
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Please cite the following references:
GR Bowman, X Huang, and VS Pande. Methods 2009. Using generalized ensemble
simulations and Markov state models to identify conformational states.
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MSMBuilder2: Modeling Conformational Dynamics
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A Fast 3 x N Matrix Multiply Routine for Calculation of Protein RMSD.
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{'input_dir': '/home/rmcgibbo/local/msmbuilder/Tutorial/XTC',
'min_length': 0,
'pdb': '/home/rmcgibbo/projects/met-enkephalin/1PLX-0-solvated.pdb',
'project': 'ProjectInfo.yaml',
'quiet': False,
'rmsd_cutoff': -1,
'source': 'file',
'stride': 1}
16:22:45 - WARNING: Sorting trajectory files by numerical values in their names.
16:22:45 - Ensure that numbering is as intended.
16:22:45 - Found 100 traj dirs
Traceback (most recent call last):
File "/home/rmcgibbo/.pythonbrew/venvs/Python-2.7.3/sci/bin/ConvertDataToHDF.py", line 5, in <module>
pkg_resources.run_script('msmbuilder==2.7.dev', 'ConvertDataToHDF.py')
File "/home/rmcgibbo/.pythonbrew/venvs/Python-2.7.3/sci/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 489, in run_script
File "/home/rmcgibbo/.pythonbrew/venvs/Python-2.7.3/sci/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 1207, in run_script
File "/home/rmcgibbo/.pythonbrew/venvs/Python-2.7.3/sci/lib/python2.7/site-packages/msmbuilder-2.7.dev-py2.7-linux-x86_64.egg/EGG-INFO/scripts/ConvertDataToHDF.py", line 136, in <module>
args.min_length, args.stride, rmsd_cutoff)
File "/home/rmcgibbo/.pythonbrew/venvs/Python-2.7.3/sci/lib/python2.7/site-packages/msmbuilder-2.7.dev-py2.7-linux-x86_64.egg/EGG-INFO/scripts/ConvertDataToHDF.py", line 70, in run
pb.get_project().save(projectfn)
File "/home/rmcgibbo/.pythonbrew/venvs/Python-2.7.3/sci/lib/python2.7/site-packages/msmbuilder-2.7.dev-py2.7-linux-x86_64.egg/msmbuilder/project/builder.py", line 128, in get_project
self.convert()
File "/home/rmcgibbo/.pythonbrew/venvs/Python-2.7.3/sci/lib/python2.7/site-packages/msmbuilder-2.7.dev-py2.7-linux-x86_64.egg/msmbuilder/project/builder.py", line 159, in convert
traj = self._load_traj(file_list)
File "/home/rmcgibbo/.pythonbrew/venvs/Python-2.7.3/sci/lib/python2.7/site-packages/msmbuilder-2.7.dev-py2.7-linux-x86_64.egg/msmbuilder/project/builder.py", line 221, in _load_traj
discard_overlapping_frames=True)
File "/home/rmcgibbo/.pythonbrew/venvs/Python-2.7.3/sci/lib/python2.7/site-packages/msmbuilder-2.7.dev-py2.7-linux-x86_64.egg/msmbuilder/Trajectory.py", line 396, in load_from_xtc
raise ValueError('The coordinate data contains %d atoms, but the topology contains %d atoms. Did you supply the wrong topology perhaps?' % (A["XYZList"].shape[1], A['AtomNames'].shape[0]))
ValueError: The coordinate data contains 22 atoms, but the topology contains 2571 atoms. Did you supply the wrong topology perhaps?
I actually was using an older version now that I look at it. Don't know how I ended up with that one rather than the newest one but you're right. My mistake!
No problem.
I was trying to use ConvertDataToHDF.py and kept getting this error:
IndexError: index (988) out of range (0<=index<987) in dimension 1
It turns out my problem was that I was using a pdb with waters still in it (more than 988 atoms), but xtc files with waters stripped (988 atoms). Still, this doesn't seem like too noob-friendly an error message with what seams like an easy mistake to make.