I would be glad to hear you suggestions then. Please do let me know.
Let me reply this. This is exactly what I am working on right now.
From: Users of GLYCAM & GLYCAM-Web <[log in to unmask]> on behalf
of Samuel Walpole (PHA) <[log in to unmask]>
Sent: Wednesday, May 11, 2016 4:10:11 AM
To: [log in to unmask]
Subject: Xylose Ring Conformation Problem
Dear Glycam Users,
I am currently working on a system involving an oligosaccaharide containing a xylose residue. I notice that during my simulations the xylose ring flips from the 4C1 to the 1C4 conformation during the simulation and remains this way for the remainder of the simulation. However, the predominant ring conformation for xylose should be 4C1, and indeed I have seen this problem reported previously for xylose using Glycam, although no solution was suggested. I was thinking of applying some sort of restraint to this residue to prevent the ring from flipping, but I am not sure what is the best way to implement this. I would be very grateful for any suggestions.
Sam Walpole, PhD Student
School of Pharmacy
University of East Anglia
Norwich Research Park