Are you sure this is a valid GROMACS xtc file?

[Qwarctick]

Hi,

I have a problem when I try to run your command python ../scripts/test_kcenters.py -n 500. on your dataset.

Python returns this error:

..
stride: None
Reading trajs...
Reading:  ./XTC/RUN00/frame0.xtc
Reading:  ./XTC/RUN00/._frame0.xtc
Traceback (most recent call last):
  File "../scripts/test_kcenters.py", line 48, in <module>
    trajreader = XTCReader(trajlistname, atom_indicesname, homedir, trajext, File_TOP, nSubSample=stride)
  File "../utils/reader_.py", line 71, in __init__
    self.trajs, self.traj_len = self.read_trajs(self.framefile_list)
  File "../utils/reader_.py", line 82, in read_trajs
    stride=self.nSubSample)
  File "/home/pnoel/py_HK/local/lib/python2.7/site-packages/mdtraj/core/trajectory.py", line 362, in load
    value = loader(filename, **kwargs)
  File "mdtraj/formats/xtc/xtc.pyx", line 141, in xtc.load_xtc
  File "mdtraj/formats/xtc/xtc.pyx", line 232, in xtc.XTCTrajectoryFile.__cinit__
IOError: Malformed XTC file. Number of atoms <= 0. Are you sure this is a valid GROMACS xtc file?

Do you have a solution to the problem? The list of libraries installed in my environment are as follows:

backports.functools-lru-cache (1.4)
cycler (0.10.0)
Cython (0.27.3)
matplotlib (2.1.2)
mdtraj (1.3.0)
msmbuilder (3.8.0)
numpy (1.9.2)
pip (9.0.1)
pyparsing (2.2.0)
python-dateutil (2.6.1)
pytz (2017.3)
scikit-learn (0.16.1)
scipy (0.15.1)
setuptools (2.2)
six (1.11.0)
subprocess32 (3.2.7)

thank you in advance