From: Mayne, Christopher G (
Date: Wed Aug 13 2014 - 12:57:38 CDT

This problem is fixed (without requiring the NAMD flag) in the VMD 1.9.2alpha builds. I don't remember if the NAMD flag solution is in the 1.9.1 release.

Christopher Mayne

On Aug 13, 2014, at 12:50 PM, "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.