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Dear Olivier,

Thank you .That was really helpful, i'll try to reach out for more help
with the guys who made do_glycans.
If it doesn't work i'll try using Amber as you recommended.

Le mer. 20 mars 2019 à 14:12, Oliver Grant <[log in to unmask]> a
écrit :

> 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*
>> *Email: [log in to unmask] <[log in to unmask]>*
>>
>>
>

-- 
*Monia KAMLY,*

*Ingénieur en Chimie Analytique et Instrumentation,*
*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*
*Email: [log in to unmask] <[log in to unmask]>*