VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Wed Aug 13 2014 - 14:36:47 CDT

Sounds like I was incorrect re not requiring the NAMD flag. Sorry for the error.

On Aug 13, 2014, at 12:57 PM, Mayne, Christopher G wrote:

> 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" <vermaas2_at_illinois.edu> 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.
>>
>