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Amber-MD / cpptraj

Biomolecular simulation trajectory/data analysis.
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Allow reading of badly formatted PSF files #1033

Closed drroe closed 1 year ago

drroe commented 1 year ago

Version 6.19.4.

Some PSF files (such as those written by VMD) can be badly formatted (for example, missing the segment ID column in the NATOM section), e.g.:

  130676 !NATOM
       1      1    ASP  N    N3     0.078200       14.0100           0

This PR allows cpptraj to recognize and successfully read these PSF files. Under the hood switches from using CpptrajFile to BufferedLine class for reading.

drroe commented 1 year ago

Jenkins failure is another inexplicable pytraj one. Noted in https://github.com/Amber-MD/pytraj/issues/1633