Open kellegra opened 2 years ago
Okay, I checked what the align.py of the MDAnalysis package is actually doing. It seems that there is an issue with the selection I did for the auxi_selection used in tr.analysis_all_namd() function. It fails with the reported error when using
auxi_selection = ["backbone"]
I changed the selection to
auxi_selection = ["((resid 1:353) and (name C CA N))"]
what made the whole thing working. I think there is a issue with the selection "backbone", since my protein has two phosphorylated residues, but not sure if this is really causing the problem.
In the end, the different selection made it.
Hi there,
I am trying to analyze a trajectory object. Running a single trajectory passes and all plots can be generated. But when using the trajectory object by using tr.analysis_all_namd() it throws out the error shown in the bottom. Not sure how to deal with this, since other trajectories work. The trajectories that worked, were generated following the gromacs-ramd workflow. The trajectories that do not work were generated following the the initial RAMD paper from 2018. But not sure, why this would end up in this issue.
I hope, you have any ideas how I could fix this problem.
Best regards, Gerald