I created a single DGDG molecule (digalactosyldiacylglycerol) in Pymol.
The next step is:
Once structure of first molecule is prepared, it must be aligned
so that its main axis is parallel to the z-direction, e.g., acyl chains
along z-axis, so the head group is placed down in the absolute
reference system (this direction is the one assumed in this
example for the initial DPPC molecule). In order to simplify
this and the following steps it is a good practice to draw the acyl
chains in their extended positions and parallel one to the other,
so that the lipid takes the minimum space in the xy-plane.
$ editconf -f DPPC.pdb -o DPPC_rot.gro -rotate X Y Z -box
0.96 0.96 2.20
(a) “X,” “Y,” and “Z” are degrees of rotation around each axis
and they depend on the original positioning of the DPPC
molecule when drawn. Often the correct values for “X,”
“Y,” and “Z” are found through a process of trial and error.
For example my coordinates at the end of acyl chain (atom C51)is:
x=-14.720 y=-7.537 z=9.164
and my coordinates of atom in head group (for example atom C13) is:
x=-14.931 y=19.131 z=2.012
Which rotation can be the best in that example? I think probably y should be minus in head group, so I can create a down-layer. X probably is ok, but Z?
gmx editconf -f DPPC.pdb -o DPPC_rot.gro -rotate 0 180 ?Z? -box
0.96 0.96 2.20
I use this article for guide to modelling bilayer Article Molecular Dynamics Simulations of Lipid Bilayers: Simple Rec...
There are some webservers that can help you to assemble lipids into a bilayer: http://compbio.clemson.edu/sapp/problm_webserver/ , http://bioinf.modares.ac.ir/software/mb2/
Dear Jakub,
I can recommend you "packmol-memgen" that is distributed with AmberTools18. Please check the Amber manual for further informations (http://ambermd.org/doc12/Amber18.pdf).
Best Regards,
Benedikt
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