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
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