[gmx-users] Rhamnose on 53a6
Mark.Abraham at anu.edu.au
Mon Jun 11 10:17:28 CEST 2012
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.
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