Unable to read PSF file generated with VMD AutoPSF plugin

[biomolsim]

I generated a PSF file with the VMD AutoPSF plugin, and I am receiving the following error. Could anyone please let me know how to resolve this? Thank you very much.

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
File ~\anaconda3\envs\prolif\lib\site-packages\MDAnalysis\core\universe.py:110, in _topology_from_file_like(topology_file, topology_format, **kwargs)
    109     with parser(topology_file) as p:
--> 110         topology = p.parse(**kwargs)
    111 except (IOError, OSError) as err:
    112     # There are 2 kinds of errors that might be raised here:
    113     # one because the file isn't present
    114     # or the permissions are bad, second when the parser fails

File ~\anaconda3\envs\prolif\lib\site-packages\MDAnalysis\topology\PSFParser.py:109, in PSFParser.parse(self, **kwargs)
    108     logger.error(err)
--> 109     raise ValueError(err)
    110 header_flags = header[3:].split()

ValueError: <path_to_file> is not valid PSF file (header = NAMD PSF
)

During handling of the above exception, another exception occurred:

ValueError                                Traceback (most recent call last)
Cell In[41], line 1
----> 1 u = mda.Universe(psf_file)

File ~\anaconda3\envs\prolif\lib\site-packages\MDAnalysis\core\universe.py:356, in Universe.__init__(self, topology, all_coordinates, format, topology_format, transformations, guess_bonds, vdwradii, fudge_factor, lower_bound, in_memory, in_memory_step, *coordinates, **kwargs)
    354 if not isinstance(topology, Topology) and not topology is None:
    355     self.filename = _check_file_like(topology)
--> 356     topology = _topology_from_file_like(self.filename,
    357                                         topology_format=topology_format,
    358                                         **kwargs)
    360 if topology is not None:
    361     self._topology = topology

File ~\anaconda3\envs\prolif\lib\site-packages\MDAnalysis\core\universe.py:125, in _topology_from_file_like(topology_file, topology_format, **kwargs)
    121         raise IOError("Failed to load from the topology file {0}"
    122                         " with parser {1}.\n"
    123                         "Error: {2}".format(topology_file, parser, err))
    124 except (ValueError, NotImplementedError) as err:
--> 125     raise ValueError(
    126         "Failed to construct topology from file {0}"
    127         " with parser {1}.\n"
    128         "Error: {2}".format(topology_file, parser, err))
    129 return topology

ValueError: Failed to construct topology from file <path_to_file> with parser <class 'MDAnalysis.topology.PSFParser.PSFParser'>.
Error: <path_to_file> is not valid PSF file (header = NAMD PSF
)

[orbeckst]

The specification of the PSF format that the MDAnalysis PSFParser implements says that the header line starts with PSF. It may contain other "flags" such as "CMAP", "EXT" (or NAMD) following it (e.g. PSF NAMD CMAP). The NAMD tutorial, when talking about PSF files, also indicates that the header starts with PSF.

From our current perspective, VMD AutoPSF produced an incorrectly formatted PSF file. Do you have any indication that the VMD AutoPSF produces correct PSF files that are readable by other tools (which ones?)?

You can try to manually fix the header line in your file by rewriting it in a text editor to PSF NAMD, or use something like sed "1s/NAMD PSF/PSF NAMD/" my.psf > fixed.psf

[biomolsim]

I changed the order, and now it even works without a NAMD term. The elements column was missing, and adding it to the universe resolved any further issues regarding the PSF file.

from MDAnalysis.topology.guessers import guess_types

guessed_elements = guess_types(universe.atoms.names)
universe.add_TopologyAttr('elements', guessed_elements)