[gmx-users] Problem with Glucose ring

[Patel Ronak Y]

Dear Gromacs users.

I have prepared sugar topology files for galactose, N-acetyl galactosamine
GalNAc) and glucose. I have carried out some simulations.

The problem that occurs is, during simulations the Glucose ring
conformation (chair conformation) get skewed up. The Galactose and GalNAc
nicely maintain the chair conformation.

I have checked topology files many and many times, I have plotted angle,
dihedrals, improper dihedrals also. Everything seem to be fine and around
equilibrium values.

An interesting thing to note is that galactose and glucose varies only at
C4 position. In my simulations, the galactose ring is stable in chair
conformation and glucose ring is in somewhat skewed chair conformation.
Can somebody give suggestion what might be the reason?

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Patel Ronak Y.
School of Bioscience and Bioengineering,
Indian Institute of Technology Bombay,
Mumbai-400076
Maharashtra
India.

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