VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 13 2014 - 12:21:27 CDT

Hi,
  There are neverending misunderstandings of the format(s) of PSF files.
The original PSF formats were those used by CHARMM and XPLOR, both of
which used (and to a large extent _still_ use) Fortran based I/O that
depended on fixed column widths for the different fields. Other tools
such (NAMD is one such example) have implemented variants of the PSF format
that are more liberal, allowing arbitrary amounts of whitespace between
records, and other variations such as the use of strings rather than
numeric indices for some information, and so on. VMD has the challenge of
correctly parsing all of the different PSF variants that exist in the field,
and this is made difficult when the individual software packages that
write these PSF variants do not clearly label them as such.

To this end, we have changed both NAMD and VMD so that the free-form whitespace
deliminated PSF variant used by NAMD is clearly labelled as such using the
new "NAMD" tag, located within the PSF header. This makes the formatting
distinct from other variants (e.g. CGenFF) generated by CHARMM and
other tools, and allows VMD to parse all of them correctly. This change
is in the newest test versions of NAMD and VMD, but is not implemented
in the prior versions.

The change became necessary when CGenFF and other
CHARMM features became widely used, and the existing PSF variants started
to become otherwise-indistinguishable from each other, from the perspective
of a PSF file parser reading the first parts of the file header. In any
case, this is not so much an issue of VMD or any other program having a
"bug", but rather an issue created by the diversity of format variants that
live under the "PSF" file format umbrella, combined with the fact that
the teams of developers of each of the molecular dynamics tools work
largely independently and there is no centralized group of people
maintaining a unified "PSF" format standard. So for now, and until
the PSF file format is completely superceded, these issues will likely
continue to crop up again in the future as further variants are invented.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 13, 2014 at 12:55:16PM -0400, Josh Vermaas wrote:
> Hi Alexander,
>
> The short answer is to add the NAMD flag to the top of the psf file,
> which tells VMD to use a whitespace-based file reader instead of a
> column-delimited one. (PSF NAMD <other flags> instead of PSF <other
> flags>) Where did this PSF come from? Its been a while since I checked,
> but I thought VMD handled the usual ways these files get made (CHARMM,
> using the extended file format) without truncating the columns, although
> I've been using the beta builds for so long I sometimes forget what bugs
> are lurking in 1.9.1.
>
> -Josh Vermaas
>
> On 8/13/14, 11:59 AM, Alexander Balaeff wrote:
> >Dear VMD gurus:
> >
> >Could anyone kindly advise me on the right way to read a PSF file
> >where the atom types are longer than the classical 4 characters? (for
> >example, the 5- and 6-letter atom types produced by CGenFF) The
> >default PSF reader in VMD is apparently column-based so when the
> >nonstandard PSFs are read, the atomic charges are read incorrectly. Is
> >there a flag in VMD or the mol command, or maybe a separate plugin,
> >that would allow one to read the PSFs with CGenFF types?
> >
> >Thanks a lot,
> >
> >Alexander.
> > 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/