VMD-L Mailing List

From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Mon Feb 05 2024 - 09:25:25 CST

Hi Joel,

How did you generate your psf file? All the atom names are “X”, which is weird, but I think the real reason it is bailing is your spacing. You’ve told VMD that you have an EXT psf , so that each field has a specific width. In the EXT specification, its supposed to be 8 characters + 1 space for many fields, but the space between your resname (14C) and your atom name (N1) isn’t that wide. The most expedient thing to do is probably just to tell VMD that you have a “NAMD” formatted psf, which tells VMD to use space-delimited file reading, rather than fixed widths.

So instead of “PSF EXT” at the top, you’d want “PSF NAMD”

-Josh

From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of Joel Subach <mjsubach_at_alumni.ncsu.edu>
Date: Saturday, February 3, 2024 at 10:34 AM
To: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: ffTK Opt. Charge Run Optimization Error PSF File Problem INQUIRY

Hello VMD Community:), towards the above topic:

I had entered all of the appropriate files within the ffTK Opt. Charge Tab, however,
am generating the below error upon Run Optimization:


Failed to parse atom line in PSF file:

psfplugin) ' 1 X 1 14C N1 NG2R51 -0.04 14.007 0

'

couldn't read atom 0

ERROR) molecule_structure: Unable to read structure for molecule 0

ERROR) molecule_structure: severe error indicated by plugin aborting loading of molecule 0



Attached is the matching INPUT PSF and PDB Files.



Thanks if you know:),

Joel 🚀