Dear Xiao and Rob,
Thank you both very much for your quick responses. I will give the simulation in TIP5P water a try and look forward to any future developments.
Dear Mr./Ms. Walpole,
We did notice such discrepancies for beta-D-xylopyranoside in MD simulations and NMR observations. We investigated the origin of this issue, which could result from insufficient energy barrier for ring-flip in pyranose rings. We calculated the energy barrier for tetrahydropyran (THP) in both QM and MM, and the energy barrier calculated from MM is about 2 kcal/mol lower than the one calculated from QM. We are looking into force field parameters to fix this problem.
While we are looking into this issue, we would suggest applying the TIP5P water model. We observed better agreements between MD simulations and NMR results when the TIP5P water model was applied.
When this insufficient ring flip barrier issue is fixed, I will update the solution on the listserver.
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 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