Hello everyone!
APL analysis needs renames and a selection of atoms from each resname for each lipid type.
But I'm not sure how to choose atoms for each lipid type.
Apparently, it can be a single atom or a triad of atoms, but what atoms should I select for each lipid type?
What are the circumstances for selecting atoms?
How much does selecting atoms affect the final results?
I really appreciate any help you can provide.
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The Area per Lipid tool calculates both the total area per lipid and the area per lipid of each lipid species of the membrane under analysis. To this end, it uses a user-customizable selection of one key atom (e.g. sterols) or a triad of atoms (e.g. phospho- or sphingolipids). The x and y coordinates of the former set of points are projected onto a plane delimited by the simulation box, which is subsequently divided into polygons through a ** Voronoi diagram** using the qvoronoi program from the Qhull package (Barber et al., 1996). Thereby, the area of each polygon is calculated.
Hence, the specified set of atoms should share the same plane in the simulation as the others, and need to tend to remain in the same plane during the whole simulation.
The atoms chosen here are the centre of the negatively charged region (phospholipids) and the centre of the polar region (sphingomyelin) respectively.
For cholesterol is the polar head.
The set of atoms to be used is highly dependent on where those atoms tend to be situated along the thickness of the membrane, according to the physiochemical properties of the whole molecule (charge, hydrophobicity, polarity, shape...), and also the plane formed by the 3 atoms should align as much as possible to the membrane plane during the simulation.
Also it is recommended to use non-hydrogen atoms as hydrogen atoms tend to move more creating noise.
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So, I should select an atom or a triad of atoms in the same membrane depth. Also, the plane of the triad of atoms must be parallel to the main plane of the membrane.
Am I getting this right?
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Yes, that's it. But, the plane of the triad of atoms being parallel to the main plane of the membrane is not so important if the atoms of the triad from the same molecule are close to each other.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hello everyone!
APL analysis needs renames and a selection of atoms from each resname for each lipid type.
But I'm not sure how to choose atoms for each lipid type.
Apparently, it can be a single atom or a triad of atoms, but what atoms should I select for each lipid type?
What are the circumstances for selecting atoms?
How much does selecting atoms affect the final results?
I really appreciate any help you can provide.
The Area per Lipid tool calculates both the total area per lipid and the area per lipid of each lipid species of the membrane under analysis. To this end, it uses a user-customizable selection of one key atom (e.g. sterols) or a triad of atoms (e.g. phospho- or sphingolipids). The x and y coordinates of the former set of points are projected onto a plane delimited by the simulation box, which is subsequently divided into polygons through a ** Voronoi diagram** using the qvoronoi program from the Qhull package (Barber et al., 1996). Thereby, the area of each polygon is calculated.
Hence, the specified set of atoms should share the same plane in the simulation as the others, and need to tend to remain in the same plane during the whole simulation.
For example, take a look at these pictures for SDPC and SM18 https://sourceforge.net/p/membplugin/wiki/AreaPerLipid/attachment/SDPC.jpg
https://sourceforge.net/p/membplugin/wiki/AreaPerLipid/attachment/SM18.jpg
The atoms chosen here are the centre of the negatively charged region (phospholipids) and the centre of the polar region (sphingomyelin) respectively.
For cholesterol is the polar head.
The set of atoms to be used is highly dependent on where those atoms tend to be situated along the thickness of the membrane, according to the physiochemical properties of the whole molecule (charge, hydrophobicity, polarity, shape...), and also the plane formed by the 3 atoms should align as much as possible to the membrane plane during the simulation.
Also it is recommended to use non-hydrogen atoms as hydrogen atoms tend to move more creating noise.
Thank you Ismael!
So, I should select an atom or a triad of atoms in the same membrane depth. Also, the plane of the triad of atoms must be parallel to the main plane of the membrane.
Am I getting this right?
Yes, that's it. But, the plane of the triad of atoms being parallel to the main plane of the membrane is not so important if the atoms of the triad from the same molecule are close to each other.