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membrane-systems / PCAlipids

Scripts for PCA and related analyses of lipid motions
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Concatenating trajectories in tutorial #21

Open andresilvapimentel opened 3 years ago

andresilvapimentel commented 3 years ago

I am trying to run the tutorial by running the command:

!python3 pcalipids.py concat -f trajectory.xtc -t structure.pdb -l DOPC

I got the error message: Traceback (most recent call last): File "pcalipids.py", line 326, in main(args) File "pcalipids.py", line 322, in main main(*params) File "/content/PCAlipids/scr/con_traj.py", line 44, in main lipid_resname = lipid_resname, stride = stride, sf = sf, ef = ef) File "/content/PCAlipids/scr/con_traj.py", line 13, in load_traj topol = md.load(traj_top).topology File "/usr/local/lib/python3.7/dist-packages/mdtraj/core/trajectory.py", line 433, in load value = loader(filename, **kwargs) File "/usr/local/lib/python3.7/dist-packages/mdtraj/formats/pdb/pdbfile.py", line 153, in load_pdb with PDBTrajectoryFile(filename, standard_names=standard_names) as f: File "/usr/local/lib/python3.7/dist-packages/mdtraj/formats/pdb/pdbfile.py", line 269, in init self._read_models() File "/usr/local/lib/python3.7/dist-packages/mdtraj/formats/pdb/pdbfile.py", line 563, in _read_models self._topology.create_disulfide_bonds(self.positions[0]) IndexError: index 0 is out of bounds for axis 0 with size 0

Could you help me to find the error, please?

pbuslaev commented 3 years ago

Hi, could you please run pcalipids and pcalipids concat without any options and share the output please?