From: Josh Vermaas (
Date: Wed Aug 13 2014 - 11:55:16 CDT

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.