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Dear Monia,

I haven't used gromacs in years so I can't help you much, and no one else currently the Woods group has used it that I'm aware of. I haven't heard of do_glycans, but I looked it up. The research group (https://www.helsinki.fi/en/researchgroups/biophysics) that made it has published this: 
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005663,
where they do indeed use Glycam/Amber within gromacs. That has risks as you must convert properly, and it's easy to do it incorrectly and not notice.

In the supplement they say:

We then used the GROMACS tool pdb2gmx to obtain a topology for the CD44-HABD for the AMBER99SB-ILDN S7 force field. All HA structures and topologies for
the corresponding GLYCAM06h S8 force field were, on the other hand, built with a custom-
made python script. This script attaches monosaccharides sequentially in order to generate
more complex polymers, such as HA, simultaneously generating proper GROMACS topolo-
gies for them. All the generated HA structures were visually inspected to confirm the correct
structure and the stereochemistry of the carbohydrate rings and linkages. All the system
structures and corresponding topologies are publicly available in ’Zenodo.org

Perhaps that custom script became do_glycans? I would recommend reaching out to them for help with do_glycans.

As always I recommend using Amber instead of Gromacs when using Glycam/Amber as there are issues with converting the dihedral terms properly. But if you must, make sure to double-check everything. 

Best,
Oliver


On Wed, Mar 20, 2019 at 1:55 PM monia kam <[log in to unmask]> wrote:

Hello,
So i actually have an issue with the protonated version of Beta-D-Glucuronic acid for the construction of the model hyaluronic acid, so i included the version 0ZBP in the prep file GLYCAM06.prep, but then i got these following errors with grompp:
ERROR 1 [file HAP.itp, line 104]:
  No default Bond types


ERROR 2 [file HAP.itp, line 325]:
  No default Angle types


ERROR 3 [file HAP.itp, line 327]:
  No default Angle types


ERROR 4 [file HAP.itp, line 450]:
  No default Proper Dih. types


ERROR 5 [file HAP.itp, line 452]:
  No default Proper Dih. types


ERROR 6 [file HAP.itp, line 454]:
  No default Proper Dih. types


ERROR 7 [file HAP.itp, line 464]:
  No default Proper Dih. types


ERROR 8 [file HAP.itp, line 465]:
  No default Proper Dih. types

I hope you can help me with this, Thank you

PS; I used the too do_glycans in order to generate the .pdb and .itp files

--
Monia KAMLY,
Etudiante Master 2 Chimie, Spécialité, Agro-ressources Biomolécules et Innovations
Faculté des Sciences et Techniques, Université de Limoges.
123 Avenue Albert Thomas, 87000 Limoges
Mobile: 06 99 78 86 29