From: Josh Vermaas (
Date: Sun Jul 05 2020 - 15:33:12 CDT

psfgen does exactly what you tell it to, and to be honest, setting new
coordinates in psfgen is hard, so your input deck might just be weird/have
misnamed atoms in the pdb you feed to coordpdb (they need to match the
names in the psf). What does the script look like?


On Sun, Jul 5, 2020 at 10:14 AM Francesco Pietra <>

> Hello
> running psfgen from vmd in text mode, I would like that the spatial
> arrangement of an organic molecule surrounded by smaller molecule is
> conserved. Although there are no clashes among the pdd in /parts, psfgen
> displaces the bigger molecule out of the assembly of smaller molecules.
> Is any way to conserve, more or less, the initial spatial arrangement?
> thanks for advice
> francesco pietra