GLYCAM06: A Generalizable Biomolecular Force Field. Carbohydrates

GLYCAM06: A Generalizable Biomolecular Force Field. Carbohydrates

2008 March ; 29(4): 622–655. doi:10.1002/jcc.20820. | KARL N. KIRSCHNER, AUSTIN B. YONGYE, SARAH M. TSCHAMPEL, JORGE GONZÁLEZ-OUTEIRINO, CHARLISA R. DANIELS, B. LACHELE FOLEY, and ROBERT J. WOODS
The paper presents a new version of the GLYCAM force field, named GLYCAM06, which is designed to be more general and transferable for modeling carbohydrates and other biomolecules. The previous version of GLYCAM was specific to carbohydrates and AMBER force field parameters, but the new version removes these limitations. All force field terms are explicitly specified, and no default or generic parameters are used. The torsion terms in GLYCAM06 are derived from quantum mechanical data for a collection of minimal molecular fragments and related small molecules, allowing for a single parameter set applicable to both α- and β-anomers and all monosaccharide ring sizes and conformations. The authors demonstrate that fitting dihedral parameters to QM data for internal rotational energy curves generally leads to correct rotamer populations in molecular dynamics simulations and eliminates the need for phase corrections. However, they also note that this approach has limitations in certain cases. The paper includes a detailed description of the basic components of the new force field and its extension to carbohydrates, along with validation through gas-phase and condensed-phase simulations. The results show that GLYCAM06 accurately reproduces the gas-phase properties of small test molecules and the rotamer populations of key small molecules and representative biopolymer building blocks in explicit water, as well as crystalline lattice properties such as unit cell dimensions and vibrational frequencies.The paper presents a new version of the GLYCAM force field, named GLYCAM06, which is designed to be more general and transferable for modeling carbohydrates and other biomolecules. The previous version of GLYCAM was specific to carbohydrates and AMBER force field parameters, but the new version removes these limitations. All force field terms are explicitly specified, and no default or generic parameters are used. The torsion terms in GLYCAM06 are derived from quantum mechanical data for a collection of minimal molecular fragments and related small molecules, allowing for a single parameter set applicable to both α- and β-anomers and all monosaccharide ring sizes and conformations. The authors demonstrate that fitting dihedral parameters to QM data for internal rotational energy curves generally leads to correct rotamer populations in molecular dynamics simulations and eliminates the need for phase corrections. However, they also note that this approach has limitations in certain cases. The paper includes a detailed description of the basic components of the new force field and its extension to carbohydrates, along with validation through gas-phase and condensed-phase simulations. The results show that GLYCAM06 accurately reproduces the gas-phase properties of small test molecules and the rotamer populations of key small molecules and representative biopolymer building blocks in explicit water, as well as crystalline lattice properties such as unit cell dimensions and vibrational frequencies.
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[slides and audio] GLYCAM06%3A A generalizable biomolecular force field. Carbohydrates