From: Peter Freddolino (
Date: Tue Nov 03 2020 - 11:07:14 CST

Hi Francesco,
Two quick questions:
First, does this work under vmd 1.9.3? I know we've seen several issues in
the development version of autopsf, and I want to see if this is one such
Second, could you please give more details on exactly how you're invoking
autopsf? What GUI or command line steps were taken?

On Tue, Nov 3, 2020 at 9:48 AM Francesco Pietra <>

> Hello
> I am trying to generate psf/pdb with autopsf/VMD 1.9.4a.38 for a
> homotrimer protein with peptide ligand, chloride ion, and water at each
> chain. There are several disulfide bridges.
> HIS was chande to HSE or HSP as appropriate.
> Any guess from the attached error log on where to search for my mistake?.
> I see that segid was not set on any of the partial output files.
> I assume that autopsf was using charmm36, however I did not add charmm36.
> Thanks for advice