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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.


Best,


Xiao


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,
Anjai