VMD-L Mailing List

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Mon Oct 22 2018 - 16:22:32 CDT

Hi Ruki,

I didn't test this, but I found the bond defined in the
"toppar_all36_carb_glycopeptide.str" file at .../toppar/stream/carb.

If you include this file as parameter file in you NAMD configuration file,
I believe that NAMD will recognize the bond.

Best

João

On Mon, Oct 22, 2018 at 3:45 PM Rune Thomas Kidmose <rtk_at_biomed.au.dk>
wrote:

> Hi joão,
>
>
> I have also been having some troubles with glycosylations in charmm36 for
> a small MDFF pipeline I am making, so I was happy to read your answer to
> Steinar.
>
>
> As you mentioned, I have already altered the "top_all36_carb.rtf" file
> by changing two RESI names" BGLCNA and BGLCN0" into BGLN.
>
>
> I then added the modded topology file (together with all the other
> ones) using the -top flag with the autopsf command in my script
>
>
> While this seems to work, as autopsf is now able to process my test PDB
> file containing a bunch of N-linked glycosylations (NAG and BMA only), I
> now got a problem with the bond between the ASN and the NAG/BGLN
>
>
> The error from MDFF/NAMD is:
>
>
> Reason: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CC321 CT1 (ATOMS
> 19331 19329)
>
> FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CC321 CT1 (ATOMS 19331
> 19329)
> Charm++ fatal error:
> FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CC321 CT1 (ATOMS 19331
> 19329)
>
> So I am guessing I need to define this specific type of bond in
> a paramter file in order to tell NAMD how to process the ASN-NAG link?
>
> How can I proceed with this? I am guessing ppl have already made
> such files maybe?
>
> Currently I am including the following paramter files in my .namd file:
>
> par_all36_lipid.prm
> par_all36_prot.prm
> par_all36_carb.prm
> toppar_water_ions_namd.str
> par_all36_cgenff.prm
> par_all36_na.prm"
>
>
> I would assume that the "par_all36_carb.prm" would be the one to alter?
> Just dont know exactly how.
>
>
> Ruki
>
>
> ------------------------------
> *Fra:* owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> på vegne af João
> Ribeiro <jribeiro_at_ks.uiuc.edu>
> *Sendt:* 22. oktober 2018 18:46
> *Til:* steinar.halldorsson_at_crick.ac.uk
> *Cc:* Vmd l
> *Emne:* Re: vmd-l: AutoPSF error with glycana (end of segment error)
>
> 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
> 

-- 
……………………………………………………...
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