VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Fri Dec 25 2020 - 12:05:00 CST

Dear Isuru,
I think it is important to understand why this bond is showing up. How did
you generate your input structure prior to feeding them into autopsf or
charmm-gui? What atoms is the bond between? Do the two subunits have the
same chain/segment name? If both of these programs are getting confused by
your input in the same way, chances are that there is something odd about
it.
Best,
Peter

On Fri, Dec 25, 2020 at 10:08 AM Isuru Herath <ish9_at_cornell.edu> wrote:

> Hello,
>
> When I try to generate a PSF file for a protein of interest using either
> AutoPSF Builder or the CHARMM-GUI, I get a file that creates a very long
> bond between the two subunits. This creates problems further down the line
> when trying to run a simulation. Does anyone have any suggestions for how
> to handle this?
>
> Thank you,
> Isuru Herath
>