Amber's Tutorial on Building Lipid Molecules

Lipids generally refer to a large class of compounds in nature that are easily soluble in organic solvents and are non-uniform in chemical composition and structure. They mainly include fatty acids and their naturally occurring derivatives (such as esters or amines), and their biosynthesis compounds related to function. The diversity of lipid structure endows lipids with a variety of important biological functions. Lipids are not only involved in regulating a variety of life activities, including energy conversion, material transportation, information recognition and transmission, cell development and differentiation, and apoptosis, etc., but also abnormal lipid metabolism is also related to certain diseases, such as arteriosclerosis, diabetes, obesity, Alzheimer's disease, and tumor occurrence and development are closely related. Therefore, it is also very important to calculate and simulate the interaction between known molecules and certain biological macromolecules.

Tutorial

The following is summarized from the Amber 16 manual.

Use GLYCAM-06 parameters to construct lipid molecules

The figure below is a simple lipid molecule, but we did not consider its axial arrangement during the construction process. The lipid bilayer is usually placed in the (x, y) plane of the rectangular coordinate system, which requires that each lipid molecule is arranged in the z direction from the hydrophilic "head" end to the hydrophobic "tail" end. This is easily accomplished by loading a template PDB file that has been correctly aligned along the z axis.

Structure of DMPCFigure 1. Structure of DMPC.

The lipid molecule we use in this tutorial is 1,2-dimyristoyl-sn-glycero-3-phosphocholine (1,2-dimyristoyl-sn-glycero-3-phosphocholine), or DMPC for short, which consists of four fragments: Choline head group CHO, Phosphate ester head group PGL, sn-1 chain myristic acid tail group MYR, sn-2 chain myristic acid tail group MY2. The molecular structure and atom numbering are shown in the figure (for clarity, hydrogen atoms and atomic charges are not shown), where the bonding points between the residues are represented by dotted lines. This tutorial will only use each fragment prep file. These prep files start in pdb format, and then use antechamber to reformat them into prep files.

Use LEAP to construct lipid molecules

In order to use the GLYCAM-06 parameter set to build a lipid molecule, you do not need to load the entire GLYCAM pre file, but it will be automatically loaded when the default leaprc.GLYCAM_06j-1 is used. Note that the lipid molecule constructed using the following command has not Align in the required direction, it may not be used to create the lipid bilayer immediately. The specific commands are as follows:
source leaprc .GLYCAM 06j-1
loadamberprep GLYCAM 06 lipids .prep
set CHO tail CHO.1.C5
set PGL head PGL.1.01
set PGL tail PGL.1.C3
lipid = sequence { CHO PGL MYR }
set lipid tail lipid.2.C2
lipid = sequence { lipid MY2 }
impose lipid {2} { {C1 C2 C3 01 163} }
impose lipid {2} { {C2 C3 01 C1 -180} }
impose lipid {2} { {C3 01 C1 C2 180) }
impose lipid {2} { {04 C1 C2 01 -60} }
impose lipid {2} { {C1 C2 01 C1 -180} }
impose lipid {2} { {(2 01 C1 C2 180} }
savepdb lipid DMPC.pdb                 
saveamberparm lipid DMPC.top DMPC.crd

* For Research Use Only.

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