From: Isuru Herath (
Date: Fri Dec 25 2020 - 21:21:28 CST

Thank you so much! Turns out it was the chain names.

On Fri, Dec 25, 2020 at 1:05 PM Peter Freddolino <> wrote:

> 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 <> 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