[gmx-users] Rhamnose on 53a6

[Mark Abraham]

On 11/06/2012 6:11 PM, Marc Gordon wrote:
> Hello again fellow gromacs users.
>
> I am looking to model a glucose-rhamnose disaccharide using the 53a6 
> forcefield. I wanted to take a look at the naming conventions for 
> carbohydrates but I'm battling to find anything in the pdb2gmx force 
> field files.

Not all force fields support sugars and even if they do, their (full) 
conversion to GROMACS can be dependent on someone taking the time to do so.

>
> I downloaded a package of force fields from the GROMOS website to get 
> an idea about naming conventions for carbohydrates and couldn't see 
> any mention of rhamnose anywhere. (allose, altrose, glucose, mannose, 
> gulose, idose, galactose and talose are mentioned but no rhamnose).
>
> Does anyone have any information on naming conventions for rhamnose or 
> whether or not rhamnose was ever present in this force field?

That sounds like a question you should answer by reading the GROMOS 
force field literature. If you'll have to make a topology yourself, 
you'll have to read those anyway.

Mark