AMBER Archive (2008)

Subject: AMBER: MM-PBSA for carbohydrates

From: Neha Gandhi (
Date: Mon May 19 2008 - 21:07:24 CDT

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
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?

Neha Gandhi

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