VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Sun Dec 05 2021 - 10:14:11 CST

What parameter files are you including, and what topology files did you use
in building the iron sulfur cluster? Most likely you don't have the
parameter file included that would contain the parameters for this cluster.
Best, Peter

On Sun, Dec 5, 2021 at 8:25 AM Kiana Jahani <kiana.jahani_at_remove_yahoo.com>
wrote:

> Dear VMD Users
>
> I generated the psf file from a pdb file using psfgen. For minimization, I
> got the following error:
> FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR FEJO SJO FEJO SJO
> (ATOMS 75913 75919 75915 75918)
> The atoms refer to iron sulfur cluster present in protein.
> I also added "auto angles dihedrals" to the psfgen script but the result
> didn't change.
> I would appreciate it if anyone can help me with that. If more information
> is required, please just let me know.
>
> Best,
> Kiana
>
>