VMD-L Mailing List

From: Steinar Halldorsson (steinar.halldorsson_at_crick.ac.uk)
Date: Mon Oct 22 2018 - 08:58:12 CDT

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

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