When running run_waterkit.py, The box parameters X Y Z, SX SY SZ can be chosen such that the trajectory (partially or completely) contains semi empty files (i.e. pdb files containing just "TER").
When subsequently running
python scripts/wk_make_trajectory.py -r my_examples/protein_prepared.pdb -w traj -o protein
There's a parmed error:
File "/Users/username/miniconda3/envs/waterkit/lib/python3.9/site-packages/parmed/formats/registry.py", line 180, in load_file
raise FormatNotFound('Could not identify file format')
parmed.exceptions.FormatNotFound: Could not identify file format
Which is rather unhelpful to understand the cause (especially if there are just a few "empty" files in the trajectory).
There should be an informative error or if possible handled in some other way (don't know whether e.g. dropping empty files is a possibility).
When running
run_waterkit.py, The box parameters X Y Z, SX SY SZ can be chosen such that the trajectory (partially or completely) contains semi empty files (i.e. pdb files containing just "TER").When subsequently running
There's a parmed error:
Which is rather unhelpful to understand the cause (especially if there are just a few "empty" files in the trajectory).
There should be an informative error or if possible handled in some other way (don't know whether e.g. dropping empty files is a possibility).