VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
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.
Best,
Peter

On Fri, Jan 24, 2020 at 3:32 AM LOKI LOKI <lokil7699_at_gmail.com> 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.
>