Extension of the GLYCAM06 biomolecular force field to lipids, lipid bilayers and glycolipids

Abstract

GLYCAM06 is a generalisable biomolecular force field that is extendible to diverse molecular classes in the spirit of a small-molecule force field. Here we report parameters for lipids, lipid bilayers and glycolipids for use with GLYCAM06. Only three lipid-specific atom types have been introduced, in keeping with the general philosophy of transferable parameter development. Bond stretching, angle bending, and torsional force constants were derived by fitting to quantum mechanical data for a collection of minimal molecular fragments and related small molecules. Partial atomic charges were computed by fitting to ensemble-averaged quantum-computed molecular electrostatic potentials.In addition to reproducing quantum mechanical internal rotational energies and experimental valence geometries for an array of small molecules, condensed-phase simulations employing the new parameters are shown to reproduce the bulk physical properties of a DMPC lipid bilayer. The new parameters allow for molecular dynamics simulations of complex systems containing lipids, lipid bilayers, glycolipids, and carbohydrates, using an internally consistent force field. By combining the AMBER parameters for proteins with the GLYCAM06 parameters, it is also possible to simulate protein-lipid complexes and proteins in biologically relevant membrane-like environments.

On the dissolution of cellulose in tetrabutylammonium acetate/dimethyl sulfoxide: a frustrated solvent

“…The cellulose was modeled using the GLYCAM06 force field (Kirschner et al 2008;Tessier et al 2008). Bonded and Lennard-Jones parameters for acetate and TBA þ were taken from the same force-field.…”

Coarse-grained model of the native cellulose $$\hbox {I}\alpha$$ and the transformation pathways to the $$\hbox {I}\beta$$ allomorph

“…The crystalline fibril of cellulose Ia was parametrized by GLYCAM-06 force field (Kirschner et al 2008;Tessier et al 2008). A solvation box was used with 120 000 TIP3P water molecules Jorgensen et al (1983) to allow for structural relaxation of the ideal crystalline structure prepared with the cellulose-builder toolkit (Gomes and Skaf 2012).…”

Intramolecular hydrogen bonding in articaine can be related to superior bone tissue penetration: A molecular dynamics study

“…Positional restraints were applied to the lipids lining the simulation box in order to conserve area per lipid during density adjustment before constant volume was used for production runs. The NVT ensemble has previously been applied to successfully simulate lipid membranes with Amber [26]. In addition, Prates et al [51] applied a similar setup to simulate articaine in presence of a POPC lipid bilayer.…”

“…The challenge faced is reflected in difficulties in reproducing experimental findings in membrane simulations. One such difficulty is to reproduce the area per lipid without either adding surface tension [19][20][21][22][23] or using constant volume [24][25][26] or fixed crosssectional area [27][28][29][30][31]. Nevertheless, experimentally validated areas per lipid have recently been achieved in tensionless constant pressure simulations of phosphatidylcholine bilayers with CHARMM [32][33][34] and GROMOS [35] force fields.…”