VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Sun Mar 03 2019 - 05:18:15 CST

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