[gmx-users] Carbohydrate GAG simulations

[Lara rajam]

Dear Neha !

Thank you for the reply .I am happy that you gave all possible ways to do
it .
It will be definitely helpful for a beginner like me.




On Thu, Sep 3, 2015 at 11:36 PM, Neha Gandhi <n.gandhiau at gmail.com> wrote:

> Hi Lara,
>
> I have worked extensively on GAGS in particular heparin. You may wish to
> refer to my publications.
>
> Glycam has residues for sulphated glucuronic acid/iduronic acid as well as
> sulphated glucosamine. You can build topologies for heparin using glycam
> webserver. If you wish to run your simulation in GROMACS, you can convert
> glycam amber topologies to gromacs format using Acpype.
>
> There are no direct parameters in GROMOS force fields to build sulfated
> GAGs (although parameters exist for hexapyranoses). Hugo Verli has used
> GROMOS force fields to simulate heparin oligosaccharide. Kindly refer to
> his publications for parameters for GAGs.
>
> CHARMM has parameters for GAGs like CS, DS but they lack parameters for
> N-sulfated glucosamine. You can use Charmm-gui to obtain parameters.
>
> I hope this helps,
>
> Best,
> Neha
>
> On 4 September 2015 at 08:54, Lara rajam <lara.4884 at gmail.com> wrote:
>
> > Dear Users !
> > I would like to do a GAG ( heparin simulation ) with gromacs. can any one
> > tell me the appropriate links related to this
> > that will be useful for a beginner like me
> >
> > thank you !
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>
> --
> Regards,
> Dr. Neha S. Gandhi,
> Curtin Research Fellow,
> School of Biomedical Sciences,
> Curtin University,
> Perth GPO U1987
> Australia
> LinkedIn
> Research Gate
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