Hi all,
This is more or less a follow up of my emails yesterday, under the topic
"X-PLOR formatted .psf in CHAMBER".
I've found a couple of issues with how ptraj deals with .PSF files. The .PSF
files I've noticed this with were generated by VMD (X-PLOR format), but I
think issue 2 may also be present with CHARMM .PSF files.
1) If the first line of the .PSF file is only "PSF" (i.e. no second string),
ptraj doesn't recognize it as a PSF file.
This could be an easy fix of course, but it could be argued that you don't
want to fix it, as this may not be a properly formatted PSF file; (more
current versions of) CHARMM don't write PSF files with only "PSF" as the
first line.
2) When the atom section (!NATOM) starts with multiple segments with only 1
residue per segment, i.e. the residue numbers are 1, ptraj interprets this
as 1 residue: the atoms are all preserved, but are given the residue name of
the first residue in the PSF (and residue number 1).
This is a more serious issue, IMO, and would be worth fixing, perhaps.
That's it for now,
Marc
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Received on Fri Sep 16 2011 - 03:30:02 PDT
