AMBER Archive (2008)

Subject: Re: AMBER: MM-PBSA for carbohydrates

From: Navnit Kumar Mishra (
Date: Tue May 20 2008 - 06:25:20 CDT

Hello Neha;

I believe the method is quit good to see the detail insight of the
interactions instead of accurate free energy predication. :-) However,
for accurate calculation of the interaction energy the method strongly
depends on two issues, first structural equilibriation is very important
for proper sampling of the conformation, and the second issue is
parameters. We have discussed in our coming paper, how the sampling
affects the interaction energy, and also we got good results in
accordance with ITC. One should also careful about the dielectric
constant, you should include the intramolecularhydrogen bonding in sugar
molecules using interanl dielectric constatn for the sugar is around 1
and 2. About the first paper by woods et. al. group they have calculated
the interaction energy by GBSA approach, where again the born radii has
influence on the binding energy, but as you can see they could able to
produce good trend of binding energy. In the second paper from first
look it seems that the calculated binding free energy is in micro and
nano molar range. I hope it would be helpful for your work.

with regards,

Neha Gandhi wrote:

> Hi All,
> I came across two papers where MM/PBSA is reported for free energy
> analysis of carbohydrates.
> 1. Molecular dynamics simulations of galectin-1-oligosaccharide
> complexes reveal the molecular basis for ligand diversity
> Michael G. Ford, Thomas Weimar, Thies Köhli^ , Robert J. Woods
> 2. MM-PBSA free energy analysis of endo-1,4-xylanase II
> (XynII)–substrate complexes: binding of the reactive sugar in a skew
> boat and chair conformation
> Tuomo Laitinen,a Juha Rouvinen b and Mikael Peräkylä
> If we look at the free energy of binding predicted (which is very
> lower), it would result into dissociation constants in pico molar. Is
> it possible that the method fails in terms of solvation calculations?
> --
> Regards,
> Neha Gandhi

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