VMD-L Mailing List

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Mon Oct 22 2018 - 11:46:39 CDT

Thank you, Steinar.

Autopsf renames NAG to BGLN automatically. In CHARMM36, there is no "BGLN"
residue, as all NAG residues have more than 4 character length residue
names (not allowed in the pdb format). To properly use autopsf with NAG,
you would need to change the target residue name in the top_all36_carb.rtf
file to BGLN, and feed it to autopsf. If your protein is heavily
glycosylated (which seems it is the case), I would also consider building
your system outside of autopsf, as the inclusion of glycans can be a little
bit tricky, and we might probably need to increase the glycan support in
autopsf.

I hope this helps

Best

João

On Mon, Oct 22, 2018 at 10:16 AM Steinar Halldorsson <
steinar.halldorsson_at_crick.ac.uk> wrote:

> Hi Joao
>
> I probably should have checked there before, here is the error message:
>
> -----
> psfgen) building segment AG1
> psfgen) reading residues from pdb file fitted_1flc_autopsf-temp.pdb_AG1.pdb
> psfgen) unknown residue type BGLN
> psfgen) extracted 2 residues from pdb file
> psfgen) setting patch for first residue to none
> psfgen) setting patch for last residue to none
> psfgen) Info: generating structure...psfgen) unknown residue type BGLN
> failed!
> -----
>
>
> Segment AG1 is the first glycan encountered and the three types of glycans
> there are NDG, NAG and a BMA. I'm not sure if BGLN corresponds to NDG?
>
>
> Thanks,
>
> Steinar
> ------------------------------
> *From:* João Ribeiro <jribeiro_at_ks.uiuc.edu>
> *Sent:* 22 October 2018 16:05:01
> *To:* Steinar Halldorsson
> *Cc:* Vmd l
> *Subject:* Re: vmd-l: AutoPSF error with glycana (end of segment error)
>
> 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
>
> Best
>
> João
>
> On Mon, Oct 22, 2018 at 8:58 AM Steinar Halldorsson <
> steinar.halldorsson_at_crick.ac.uk> 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
> http://www.ks.uiuc.edu/~jribeiro/
> jribeiro_at_ks.uiuc.edu
> +1 (217) 3005851
>
> 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
http://www.ks.uiuc.edu/~jribeiro/
jribeiro_at_ks.uiuc.edu
+1 (217) 3005851