Dear Anjai,

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.



Xiaocong Wang
Complex Carbohydrate Research Center
The University of Georgia
315 Riverbend Road,
Athens, GA, 30602
Tel: (706) 254-7958
E-mail: [log in to unmask]

From: Users of GLYCAM & GLYCAM-Web <[log in to unmask]> on behalf of Anjaiah Nalaparaju <[log in to unmask]>
Sent: Monday, August 1, 2016 5:28:24 AM
To: [log in to unmask]
Subject: GLYCAM parameters for Mannuronic acid !
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.
Best regards,