kzinovjev / string-amber Goto Github PK

When trying to run reorder_trj.py script we get this following error and it occurs in at least two different systems:

"Error: NetCDF file has no frames.
Error: Could not set up '.reorder_trj_tmp/17_87.nc' for reading.
Error: Could not set up input trajectory '.reorder_trj_tmp/17_87.nc'.
1 errors encountered reading input.
Error: Error(s) occurred during execution.
leError: NetCDF file has no frames.
Error: Could not set up '.reorder_trj_tmp/18_89.nc' for reading.
Error: Could not set up input trajectory '.reorder_trj_tmp/18_89.nc'.
1 errors encountered reading input.
Error: Error(s) occurred during execution. Error: NetCDF file has no frames.
Error: Could not set up '.reorder_trj_tmp/19_84.nc' for reading.
Error: Could not set up input trajectory '.reorder_trj_tmp/19_84.nc'.
1 errors encountered reading input.
Error: Error(s) occurred during execution.
Error: NetCDF file has no frames.
Error: Could not set up '.reorder_trj_tmp/20_82.nc' for reading.
Error: Could not set up input trajectory '.reorder_trj_tmp/20_82.nc'.
1 errors encountered reading input.
Error: Error(s) occurred during execution.
Error: NetCDF file has no frames........"

The output directory which should contain reordered trajectories typically contains only reordered string phase but one, few or none files for pmf phase.

This is due to last trajectories that the script is trying to combine seem not to have any frames.

Because of that we can't run get_ts_frames.py or resume US phase.

Any suggestions?

Thank you,

Marko