Hello All,
I want to perform drug-membrane interaction studies using Gram-negative bacterial membranes. I used CHARMM-GUI to model asymmetric mixed membranes with Lipid A in the upper leaflet and POPE:POPG: TOCL2 in the lower leaflet (representative lipids are shown below). For the average thickness of the membrane analysis, I used GridMAT-MD Perl script (provided below, column-wise) from which, I am getting doubtful values. I cross-checked with the center of mass distance from Phosphates in the upper leaflet and lower leaflet (using gmx distance), which provides satisfactory results. I got excellent ‘Z’ values if use symmetric mixed bilayers (POPE:POPG: TOCL2 in both layers), using the GridMAT-MD Perl script.
How to get proper Z values from GridMAT-MD for my membrane model? Kindly help me to resolve this issue.
Hi,
I think you will benefit from APL@Voro software:
https://sourceforge.net/projects/aplvoro2/
"APL@Voro is a program designed to aid in the analysis of lipid bilayer simulations carried out by gromacs. It calculates the area per lipid and the membrane thickness even for mixed bilayers. Colored Voronoi diagrams and different types of plots are presented in an interactive environment."
But that will also depend on what do you want to do with membrane thickness. In mixed membranes and GridMAT-MD you have to specify the phosphates atom name for all lipids, and if they have distinct names (e.g. P, PL, PLL), you must refer them all to obtain proper calculations. Usually, I give different names for all phosphates in the upper leaflet from those in the lower leaflet -> that can be the source of confusion because you have several named P.
Ricardo J Ferreira Thank you sir for your response and your suggestion.
I will definitely try the APL@Voro package.
Dr. Justin A. Lemkul's answer:
https://gromacs.bioexcel.eu/t/membrane-thickeness-using-gridmat-md/2867/9
- Badges
- Science topic