[gmx-users] Carbohydrate GAG simulations

Neha Gandhi n.gandhiau at gmail.com
Fri Sep 4 05:36:05 CEST 2015

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,


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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Dr. Neha S. Gandhi,
Curtin Research Fellow,
School of Biomedical Sciences,
Curtin University,
Perth GPO U1987
Research Gate

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