From: Francesco Pietra (
Date: Tue Nov 03 2020 - 12:52:28 CST

Hi Peter
A quick answer
As you expected, psf/pdb were built correctly with 1.9.3 (Debian Buster
amd64). I only had to rename CL ->CLA and add a stream file for ions.

Thanks a lot

On Tue, Nov 3, 2020 at 6:07 PM Peter Freddolino <> wrote:

> 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
> case.
> Second, could you please give more details on exactly how you're invoking
> autopsf? What GUI or command line steps were taken?
> Thanks,
> Peter
> On Tue, Nov 3, 2020 at 9:48 AM Francesco Pietra <>
> wrote:
>> 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