Molecular dynamics simulations of membrane-and protein-bound glycolipids using GLYCAM

Abstract

This chapter outlines protocols for the preparation, execution, and analysis of molecular dynamics (MD) simulations of glycolipids in biologically relevant environments, i.e., imbedded in lipid bilayers or bound to proteins, with the goal of generating biologically relevant structural and dynamic information. Also included is a description of ensemble average (EA) charge set development consistent with the GLYCAM06 force field and its implementation using the AMBER molecular dynamics software suite.