VMD-L Mailing List

From: Josh Vermaas (joshua.vermaas_at_gmail.com)
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?

-Josh

On Sun, Jul 5, 2020 at 10:14 AM Francesco Pietra <chiendarret_at_gmail.com>
wrote:

> 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
>