Journal
JOURNAL OF PHYSICAL CHEMISTRY B
Volume 116, Issue 36, Pages 11124-11136Publisher
AMER CHEMICAL SOC
DOI: 10.1021/jp3059992
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Funding
- NSF through XSEDE Supercomputer resources at the San Diego Supercomputer Center [TG-MCB090110]
- NSF [NSF1047875, NSF1148276, NSF1148358]
- University of California [UC Lab 09-LR-06-117792]
- Meltzer Foundation
- NIH Molecular Biophysics Training Grant [T32 GM008326]
- Office of Advanced Cyberinfrastructure (OAC)
- Direct For Computer & Info Scie & Enginr [1148276] Funding Source: National Science Foundation
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Accurate simulation of complex lipid bilayers has long been a goal in condensed phase molecular dynamics (MD). Structure and function of membrane-bound proteins are highly dependent on the lipid bilayer environment and are challenging to study through experimental methods. Within Amber, there has been limited focus on lipid simulations, although some success has been seen with the use of the General Amber Force Field (GAFF). However, to date there are no dedicated Amber lipid force fields. In this paper we describe a new charge derivation strategy for lipids consistent with the Amber RESP approach and a new atom and residue naming and type convention. In the first instance, we have combined this approach with GAFF parameters. The result is LIPID11, a flexible, modular framework for the simulation of lipids that is fully compatible with the existing Amber force fields. The charge derivation procedure, capping strategy, and nomenclature for LIPID11, along with preliminary simulation results and a discussion of the planned long-term parameter development are presented here. Our findings suggest that LIPID11 is a modular framework feasible for phospholipids and a flexible starting point for the development of a comprehensive, Amber-compatible lipid force field.
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