c36 for carbohydrates

Posted by: Nirmitee

c36 for carbohydrates - 07/24/19 02:32 PM

Hi,

I want to work with N-acetyl-D-glucosamine. The c36 toppar for carbohydrates has three entries for NAG(GlcNac).
1. AGLCNA
2. BGLCNA
3. BGLCN0

How can I know which molecule to use, if I have to compare with a GlcNac molecule from ZINC15 database?

Thanks,
Nirmitee
Posted by: rmv

Re: c36 for carbohydrates - 07/24/19 03:02 PM

BGLCN0 appears to be a special case with modified charges.

AGLCNA and BGLCNA represent alpha-GlcNac and beta-GlcNac forms, which refers to the stereochemistry at the Glc C1 position. The database ought to indicate which one.
Posted by: Nirmitee

Re: c36 for carbohydrates - 07/24/19 04:45 PM

Thank you!