From: Francesco Pietra (
Date: Mon Jul 06 2020 - 04:39:22 CDT

Sometimes one has to beg pardon for wasting time of other people. This is
this case here. I had not adjusted the atom names of the central molecule
to those in the param file. Actually, I had checked the matter several
times before posting but I must have been in a loop.


On Sun, Jul 5, 2020 at 10:33 PM Josh Vermaas <>

> 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 <>
> 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