MDAnalysis Universe error on PSF files

[mackevinbraza]

Hello all,

I want to ask for help in debugging an MDAnalysis universe error (reading PSF). I have these two PSFs where file QMESA works but PGFSA does not. I attached the two PSF file here. I generated them from cpptraj, where I stripped water, ions, and membrane.

zipfile.zip

When I read these PSF in MDanalysis, the following error appeared

ValueError: Failed to construct topology from file /net/gpfs-amarolab/PGFSA.stripped.step5_input.psf with parser <class 'MDAnalysis.topology.PSFParser.PSFParser'>.
Error: Expected section NPHI but found 5

The PSF files worked well when I load them in VMD along with the trajectories from my MD simulations.

Not sure on what else can I do to debug this or if there are other things I can do.

Do you know how I can debug this properly?

Thank you so much!

Sincerely,
Kevin

[orbeckst]

In your file PGFSA.stripped.step5_input.psf somehow a newline is missing before 8443:

    3117    3115    3121    3115    3121    3122    3115    3121    3123
    3122    3121    3123
    8443 !NPHI: dihedrals
       1       5       7       8       2       1       5       6
       2       1       5       7       2       1       5      15

When I manually rewrite it to

    3122    3121    3123
    
    8443 !NPHI: dihedrals
       1       5       7       8       2       1       5       6

then MDAnalysis can read it.

Will have to look if PSF must have a newline there (then it's a bug in the code you're using) or if MDAnalysis is to strict (then it's a bug in MDAnalysis).