Error: Your tpx version is 134, which this parser does not support, yet

[hariseldon99]

Expected behavior

Successful import of GROMACS trajectory file using tpr file as topology

Actual behavior

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

File ~/gitrepos/mdanalysis/package/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 ~/gitrepos/mdanalysis/package/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 ~/gitrepos/mdanalysis/package/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 134, which this parser does not support, yet 

During handling of the above exception, another exception occurred:

ValueError                                Traceback (most recent call last)
Cell In[2], line 1
----> 1 u = mda.Universe("md500.tpr","md500.xtc")

File ~/gitrepos/mdanalysis/package/MDAnalysis/core/universe.py:417, in Universe.__init__(self, topology, all_coordinates, format, topology_format, transformations, guess_bonds, vdwradii, fudge_factor, lower_bound, in_memory, context, to_guess, force_guess, in_memory_step, *coordinates, **kwargs)
    415 if not isinstance(topology, Topology) and not topology is None:
    416     self.filename = _check_file_like(topology)
--> 417     topology = _topology_from_file_like(self.filename,
    418                                         topology_format=topology_format,
    419                                         **kwargs)
    421 if topology is not None:
    422     self._topology = topology

File ~/gitrepos/mdanalysis/package/MDAnalysis/core/universe.py:128, in _topology_from_file_like(topology_file, topology_format, **kwargs)
    124         raise IOError("Failed to load from the topology file {0}"
    125                         " with parser {1}.\n"
    126                         "Error: {2}".format(topology_file, parser, err))
    127 except (ValueError, NotImplementedError) as err:
--> 128     raise ValueError(
    129         "Failed to construct topology from file {0}"
    130         " with parser {1}.\n"
    131         "Error: {2}".format(topology_file, parser, err))
    132 return topology

ValueError: Failed to construct topology from file md500.tpr with parser <class 'MDAnalysis.topology.TPRParser.TPRParser'>.
Error: Your tpx version is 134, which this parser does not support, yet 

Code to reproduce the behavior

Install development version of MDAnalysis as follows:

git clone https://github.com/MDAnalysis/mdanalysis
cd mdanalysis
pip install -e package/

Compile and install latest GROMACS build from source:

wget https://ftp.gromacs.org/gromacs/gromacs-2024.4.tar.gz
tar zxvf gromacs-2024.4.tar.gz
cd gromacs-2024.4
mkdir build && cd build
cmake .. -DGMX_GPU=CUDA -DGMX_SIMD=AVX_512
export LD_LIBRARY_PATH=/usr/local/cuda/targets/x86_64-linux/lib:$LD_LIBRARY_PATH
make
sudo make install

Run a standard MD simulation and get top.tpr and traj.xtc files as output

Then try to create an mda universe in python

import MDAnalysis as mda
u = mda.Universe(top.tpr, traj.xtc)

Current version of MDAnalysis

• Which version are you using? (run python -c "import MDAnalysis as mda; print(mda.__version__)")
  -- 2.9.0-dev0

• Which version of Python (python -V)?

• • Python 3.12.8

• Which operating system?
  -- Ubuntu 20.04.6 LTS, as well as Ubuntu 22.04.5 LTS