[gmx-users] Problem with Glucose ring

David spoel at xray.bmc.uu.se
Fri Jan 28 07:39:38 CET 2005

On Fri, 2005-01-28 at 11:27 +0530, Patel Ronak Y wrote:
> 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?
Check the pairs and the number of exclusions. Maybe there is large
exclusion inside the molecule. If your dihedrals are correct you could
even just turn off intramolecular interactions altogether. You didn't
say what force field you used.
> --------------------------------------------------------------------------
> Patel Ronak Y.
> School of Bioscience and Bioengineering,
> Indian Institute of Technology Bombay,
> Mumbai-400076
> Maharashtra
> India.
> --------------------------------------------------------------------------
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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