XTC file not recognized with extract_coordinates

[piia600]

Hi,

I am trying to read my files in, and I keep running into problems with the trajectories.

I have Amber trajectories in .xtc format (from cpptraj), and either pdb or prmtop for the topology. I also tried to make .psf file with Parmed, but this was not recognized by extract_coordinates as a "proper .psf file".

So the command

extract_coordinates(ref_file, pdb_file, "my_trj.xtc", "my_trj", sel_base)

leads to an error

TypeError: Cannot find an appropriate coordinate reader for file '.'.
           Unknown coordinate trajectory format '' for '.'. The FORMATs 
           dict_keys(['CHAIN', 'CHEMFILES', 'CRD', 'DCD', 'CONFIG', 'HISTORY', 'DMS', 'GMS', 'GRO', 'INPCRD', 'RESTRT', 'LAMMPS', 'DATA', 'LAMMPSDUMP', 'MOL2', 'PDB', 'ENT', 'XPDB', 'PDBQT', 'PQR', 'TRJ', 'MDCRD', 'CRDBOX', 'NCDF', 'NC', 'TRR', 'H5MD', 'TRZ', 'XTC', 'XYZ', 'TXYZ', 'ARC', 'MEMORY', 'MMTF', 'GSD', 'COOR', 'NAMDBIN', 'IN', 'FHIAIMS', 'PARMED', 'RDKIT', 'OPENMMSIMULATION', 'OPENMMAPP'])

I could open the same files as an Universe in MDAnalysis (prmtop+xtc), so it seems this issue is related to the trajectory input in extract_coordinates.

[martinvoegele]

Thanks for raising this issue, @piia600

Can you try and change your input to the following?

extract_coordinates(ref_file, pdb_file, ["my_trj.xtc"], "my_trj", sel_base)

The third argument is supposed to be a list of file names (with one element if you only have one trajectory file).

In many cases, simulations are split up into multiple subsequent jobs; that's why this behavior is the default.

[piia600]

Thanks for the quick reply!

This seems to work. I missed that the trajectory needs to be a list when all the others are just file names. I usually combine my trajctories into a single file for simplicity anyways.

I will continue my trials of trying to analyze my simulations... I doubt this will be the last issue. 😆

[martinvoegele]

Great, thanks!

I should enhance the function such that it also works if the trajectory argument is a single string.