We have valence and vdW parameters Mannuronic acid, but we don't currently have ensemble-averaged charges for it. That's why we did have it in the latest GLYCAM force field. My suggestion is calculating
Mannuronic acid's ensemble-averaged charges by following instructions in GLYCAM06 paper.
We are working on our automated ensemble-averaged charge calculation tool. Please come back and check our website soon.
Complex Carbohydrate Research Center
The University of Georgia
315 Riverbend Road,
Athens, GA, 30602
Tel: (706) 254-7958
Dear GLYCAM developers,
I would like to know if there is any standard protocol to follow if I want to simulate (MD) a oligosaccharide system whose monosaccharide units are not from the residues defined under GLYCAM forcefield (Specifically, Mannuronic acid ). I have checked all the
residue types and I think up to the current GLYCAM forcefield version acidic form residue for Mannose(Man) is not there.
I appreciate any suggestions and help.
Thanks in advance for your time.