Hello RG Community:), towards the above topic:
I had entered all of the appropriate files within the ffTK Opt. Charge Tab, however,
am generating the below errors upon Run Optimization (just the first error is included
to facilitate):
Atom name: C1 not found in molecule
Attached is the INPUT PSF and PDB Files and QM Target Data first output file: output14C+H-ACC-C1.out
I believe the molecule is referencing the pdb file which indicates the C1 atom.
Please let me know if you would need to inspect the INPUT par files.
Thanks if you know:),
Joel 🚀
...and attached is a screenshot of the output exhibiting the ffTK Console, the error message, the VMD syntax error output and the pdb file:
Hi RG Community the answer to my above inquiry below via Josh. His suggestion together with me amending my residue name to just the 3-characters 14C within both my psf and pdb files while renaming these files accordingly seems to allow the program to function, thanks gerardr as well:) 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
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