Expandtabs error

[jkmg]

Hi I am getting this error when running the following: md-sfa load-trajectories --path_to_trajectories ./md.nc --topology_file complex.pdb --stride 1

AttributeError at line 37 of /home/usuario/mambaforge/envs/MD-SFA/lib/python3.9/site-packages/md_sfa/main.py: 'NoneType' object has no attribute 'expandtabs'

I checked both the pdb and trajectory files and they are correct.

Any ideas?
Thank you

[sbhakat]

@svats73

[svats73]

Sorry for the delay on this. Seems like the issue is occurring at this line:

selection = self.topology.topology.select(atom_indices)

So it seems that the topology file is not being loaded in correctly.

import mdtraj as md
topology = md.load("path/to/topology/file")
topology.topology.select(atom_indices)

Could you let me know if this code runs properly with your topology file? My guess is that there is some issue with mdtraj loading the file.

[sbhakat]

@jkmg can you please load your topology file separately as highlighted by @svats73 and see if the code runs properly.