From: João Ribeiro (
Date: Mon Oct 22 2018 - 10:05:01 CDT

Hi Steinar,

Would it be possible to send a few lines from the VMD terminal window
before these autopsf lines? Sometimes the cause for this error is printed
before these lines.

Thank you



On Mon, Oct 22, 2018 at 8:58 AM Steinar Halldorsson <> wrote:

> Hi all
> I'm fairly new to VMD so this may turn out to be a trivial problem...!
> I'm using it for MDFF and I have a crystal structure of a glycoprotein
> which I would like to fit into a cryo-EM density. The trimeric protein has
> six modelled N-linked glycosylation sites per monomer and each site has a
> chain of three sugars, so there are lots of sugars around.
> Following the MDFF tutorial, when it comes to the AutoPSF generation I get
> this error:
> ------
> ERROR: failed on end of segment
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> ERROR: failed on end of segment
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> while executing
> "segment $segid {
> pdb $segfile
> # We alias the C-terminal OXT atoms to OT2 so that psfgen has to
> guess one atom less.
> # Otherwise psf..."
> (procedure "psfsegments" line 37)
> invoked from within
> "psfsegments $logfileout"
> (procedure "::autopsf::afterchains_gui" line 66)
> invoked from within
> "::autopsf::afterchains_gui"
> invoked from within
> ".autopsf.chains.finish invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 22)
> invoked from within
> "tk::ButtonUp .autopsf.chains.finish"
> (command bound to event)
> -------
> When I run the AutoPSF without the glycans it's fine.
> I guess this has something to do with how the AutoPSF tries to define
> different chains? There is information in the PDB file about links between
> the sugars and with the ASN, and VMD does display these links correctly.
> The types of sugars are NAG, NDG, BMA and MAN
> Has anyone run into a similar problem and found a solution? Or maybe
> someone can point me in the right direction of how to solve this problem?
> I really appreciate any help!
> Cheers,
> Steinar
> The Francis Crick Institute Limited is a registered charity in England and
> Wales no. 1140062 and a company registered in England and Wales no.
> 06885462, with its registered office at 1 Midland Road London NW1 1AT

João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
+1 (217) 3005851