From: Peter Freddolino (
Date: Fri Jan 24 2020 - 07:28:40 CST

Did you modify the topology files going into psf generation? Molefacture
lets you edit characteristics of a structure while loaded, but if you want
to make input files for MD simulations, you need a topology file for your
modified version of the residue as well. Some more information on what
exactly you're trying to change would be useful.

On Fri, Jan 24, 2020 at 3:32 AM LOKI LOKI <> wrote:

> I need to model some residue form 6di8 protein. I am using Molefracture to
> make the changes but while generating the psf it excludes the attached part
> from the structure. Is there any way to make that thing work.