Lipids Force Fields
For a full description of the force fields and how to load them, please read Chapter 3 of the Amber Reference Manual.
LIPID21 (recommended)
LIPID21 is the latest and recommended lipid force field. It extends upon the LIPID14 and LIPID17 force fields and is described in Dickson, C.J., Walker, R.C., Gould, I.R. Lipid21: Complex Lipid Membrane Simulations with AMBER, JCTC, 2022. LIPID21. LIPID21 is available in AmberTools22 and subsequent releases.
For use with earlier versions of AMBER the force field files can be downloaded using the following links:
Place these files in AMBERHOME/dat/leap/parm, AMBERHOME/dat/leap/lib and AMBERHOME/dat/leap/cmd, respectively.
LIPID21 Residue Names |
|
|---|---|
| Acyl Chain |
Res Name |
|
Lauroyl (12:0) Myristoyl (14:0) Palmitoyl (16:0) Sphingosine (16:1) Oleoyl (18:1 n-9) Stearoyl (18:0) Arachidonoyl (20:4) Docosahexaenoyl (22:6) |
LAL MY PA SA OL ST AR DHA |
| Head Group |
Res Name |
|
Phosphatidylcholine Phosphatidylethanolamine Phosphatidylserine Phosphatidylglyceroli R- Phosphatidylglyceroli S- Phosphaditic acid Sphingomyelin |
PC PE PS PGR PGS PH SPM |
| Other |
Res Name |
|
Cholesterol |
CHL |
LIPID14
- This paper describes the
primary
lipids model in Amber, lipid14.
Setting up Simulations with Lipid Bilayers
Setting up lipid bilayer simulations can be tricky. Below are a number of resources for building lipid bilayer systems.- Membrane Systems Setup
- Tutorial 5.7 Simulating A Lipid Bilayer Tutorial
- Beginning in Amber18, packmol-memgen was included into the list of available software, allowing the user to generate membrane systems in a simple and automated way. See this tutorial and Section 13.6 of the Amber Reference Manual.