VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Thu Jul 02 2020 - 19:05:20 CDT

Dear Kate,
Can you tell us what pdb you're trying to use? Does it work with a simple
example like the ubiquitin PDB from the tutorials? What text is written to
the console when you run it?
Thanks,
Peter

On Thu, Jul 2, 2020 at 7:19 PM Alilovic,Kata <alilovickata_at_ufl.edu> wrote:

> I run into an issue when creating a psf file while using Automatic PSF
> Builder. After I upload the PDB file and set the PSF builder, VMD shuts
> down and in the terminal, it says process completed. I do not get psf file
> in the end. When I load pdb file and run Automatic PSF Builder I get
> autopsf-temp_top, autopsf-temp.xbgf, and autopsf_formatted.pdb file.
> Also when I try using the Tk Console following the example given in the
> tutorial I get an error saying that it can not open the topology file and
> that molecule destroyed is destroyed by fatal error. I have the newest
> version of VMD for Mac.
> I would appreciate any advice on how to solve this.
>
>
> Best,
> *Kate*
>