VMD-L Mailing List

From: Joel Subach (mjsubach_at_alumni.ncsu.edu)
Date: Mon Feb 05 2024 - 11:32:15 CST

Hi Josh thank you for your kind update:) and your suggestions seems to be
functioning coupled to me amending my residue name
to just 14C within both my psf and pdb files while renaming the files to
just 14C as well (ffTK had generated these Xs within both my
psf and pdb files).

Best,
Joel 🚀

On Mon, Feb 5, 2024 at 4:25 PM Vermaas, Josh <vermaasj_at_msu.edu> wrote:

> 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 🚀
>
>
>
>
>
>
>