Fail to load GROMACS trajectory

[horlust]

Hello,

I am trying to load a GROMACS trajectory on MDAnalysis but I keep encountering this error:

# define universe with MDAnalysis
u  = mda.Universe('nvt_3.tpr', 'nvt_3.trr')
print(u)
print(len(u.trajectory))

---

NotImplementedError Traceback (most recent call last)
File ~/anaconda3/lib/python3.11/site-packages/MDAnalysis/core/universe.py:110, in _topology_from_file_like(topology_file, topology_format, **kwargs)
109 with parser(topology_file) as p:
--> 110 topology = p.parse(**kwargs)
111 except (IOError, OSError) as err:
112 # There are 2 kinds of errors that might be raised here:
113 # one because the file isn't present
114 # or the permissions are bad, second when the parser fails

File ~/anaconda3/lib/python3.11/site-packages/MDAnalysis/topology/TPRParser.py:212, in TPRParser.parse(self, tpr_resid_from_one, **kwargs)
211 try:
--> 212 th = tpr_utils.read_tpxheader(data) # tpxheader
213 except (EOFError, ValueError):

File ~/anaconda3/lib/python3.11/site-packages/MDAnalysis/topology/tpr/utils.py:233, in read_tpxheader(data)
232 fileVersion = data.unpack_int() # version of tpx file
--> 233 fileVersion_err(fileVersion)
235 # This is for backward compatibility with development version 77-79 where
236 # the tag was, mistakenly, placed before the generation.
237 # These versions are development versions between the 4.5 and 4.6 series.

File ~/anaconda3/lib/python3.11/site-packages/MDAnalysis/topology/tpr/utils.py:208, in fileVersion_err(fver)
207 if fver not in setting.SUPPORTED_VERSIONS:
--> 208 raise NotImplementedError(
209 f"Your tpx version is {fver}, which this parser does not support, yet "
210 )

NotImplementedError: Your tpx version is 133, which this parser does not support, yet

During handling of the above exception, another exception occurred:

ValueError Traceback (most recent call last)
Cell In[9], line 2
1 # define universe with MDAnalysis
----> 2 u = mda.Universe('nvt_3.tpr', 'nvt_3.trr')
3 print(u)
4 print(len(u.trajectory))

File ~/anaconda3/lib/python3.11/site-packages/MDAnalysis/core/universe.py:356, in Universe.init(self, topology, all_coordinates, format, topology_format, transformations, guess_bonds, vdwradii, fudge_factor, lower_bound, in_memory, in_memory_step, *coordinates, **kwargs)
354 if not isinstance(topology, Topology) and not topology is None:
355 self.filename = _check_file_like(topology)
--> 356 topology = _topology_from_file_like(self.filename,
357 topology_format=topology_format,
358 **kwargs)
360 if topology is not None:
361 self._topology = topology

File ~/anaconda3/lib/python3.11/site-packages/MDAnalysis/core/universe.py:125, in _topology_from_file_like(topology_file, topology_format, **kwargs)
121 raise IOError("Failed to load from the topology file {0}"
122 " with parser {1}.\n"
123 "Error: {2}".format(topology_file, parser, err))
124 except (ValueError, NotImplementedError) as err:
--> 125 raise ValueError(
126 "Failed to construct topology from file {0}"
127 " with parser {1}.\n"
128 "Error: {2}".format(topology_file, parser, err))
129 return topology

ValueError: Failed to construct topology from file nvt_3.tpr with parser <class 'MDAnalysis.topology.TPRParser.TPRParser'>.
Error: Your tpx version is 133, which this parser does not support, yet

It is the first time I encounter this error. Do you have any idea what it might be?

Thanks!

[hmacdope]

@horlust this should have been fixed by #4523, can you try a fresh install of develop?

[horlust]

Yep, I did:

conda install -c conda-forge \
  'Cython>=0.28' \
  'numpy>=1.21.0' \
  'biopython>=1.80' \
  'networkx>=2.0' \
  'GridDataFormats>=0.4.0' \
  'mmtf-python>=1.0.0' \
  'joblib>=0.12' \
  'scipy>=1.5.0' \
  'matplotlib>=1.5.1' \
  'tqdm>=4.43.0' \
  'threadpoolctl'\
  'packaging' \
  'fasteners' \
  'netCDF4>=1.0' \
  'h5py>=2.10' \
  'chemfiles>=0.10' \
  'pyedr>=0.7.0' \
  'pytng>=0.2.3' \
  'gsd>3.0.0' \
  'rdkit>=2020.03.1' \
  'parmed' \
  'seaborn' \
  'scikit-learn' \
  'tidynamics>=1.0.0' \
  'mda-xdrlib'

# documentation dependencies
conda install -c conda-forge 'mdanalysis-sphinx-theme>=1.3.0' docutils sphinx-sitemap sphinxcontrib-bibtex pybtex pybtex-docutils
python -m pip install docutils sphinx-sitemap sphinxcontrib-bibtex pybtex pybtex-docutils

It seems like it doesn't work on jupyter but it does on the python interpreter.

[orbeckst]

As you can see, inside Python you can find MDAnalysis!

The problem is that you are using Jupyter outside your environment. You must also install Jupyter into the same environment where all your other packages are. Otherwise Jupyter (or ipython) won’t be able to find packages inside the MDA-dev environment.

This is a very common issue when people use Jupyter and environments. The basic rule is to always install everything you need into your environment and to never try to use anything outside. You can use the commands shown above to see where exactly python modules or executables are located: they should all have a path under your envronment.

[horlust]

Oh silly me. Thanks, I think it worked! Thank you very much for your time :)

[orbeckst]

Glad that it worked! Could you then mark @hmacdope ‘s post as the answer to your question—-assuming that the MDA dev version now can read your new gmx files?

[horlust]

Done, thanks :)