Building Membrane Systems
Building Membrane Systems is tricky in Amber. A force field for the each component including lipids must be chosen. Various members of the Amber community have developed tutorials, which are listed here. Common methods to build a membrane system include using:
Lipid Force Fields
Please see the force fields page to learn about Lipid Force Fields.
Tools and Tutorials to Build Membrane Systems
PACKMOL-Memgen
By JD Callum
PACKMOL-Memgen is built into Amber.
This tutorial uses the CCG MOE GUI for protein preparation (add hydrogens, cap termini, set protonation states). You may have access to MOE or a similar GUI/tool to achieve the same task. PACKMOL-Memgen also has prep options.
Lipi21 and PACKMOL-Memgen Setup
CHARMM-GUI Setup
By Wonpil Im
Some people find it easier to set up a system for simulation in Amber using the CHARMM-GUI interface. These tutorials were written by Wonpil Im at Lehigh University. He also has You Tube videos on these tutorials.
10.2. Building Systems with CHARMM-GUI
5.7 An Amber Membrane Simulation Tutorial: Lipid14
By Benjamin D. Madej and Ross C. Walker
This tutorial explains how to set up and
simulate lipid bilayers with the Lipid14 force field and CHARMM-GUI.
This is a more general tutorial that walks you through how to build a system, equilibrate it, run MD and monitor properties.
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