VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Sun Mar 03 2019 - 22:03:55 CST

ffTK’s file writer for writing the Gaussian input files uses the element field to name the atoms; therefore, if the element field isn’t correctly set in the PDB, this is the error that you’ll see. The developers (JC and I) are aware of this bug and currently considering a fix. In the meantime, just make sure that however you’re generating the PDB sets the element correctly.

Regards,
Christopher Mayne

> On Mar 3, 2019, at 3:18 AM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov> wrote:
>
> Yup. If you load the psf file first, and then the pdb, it inherits the element field from the psf, which I think was the intended workflow.
>
> -Josh
>
>
> On 2019-03-03 01:37:08-07:00 owner-vmd-l_at_ks.uiuc.edu wrote:
>
> Hey Robin, I created this PDB myself in Avogadro, and then I opened it in VMD, saved the coordinates as a PDB again so that the formatting would be corrected. It looks like that missing column of elements is key to this problem. After running my PDB through the CGENFF website, and then using FFTK to create a new PDB and PSF, that column is there. That must be the column where FFTK grabs the atom elements from and adds them to the Gaussian file


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