I still find Packmol very tricky with parameters. I have two pdb files, one with a pre-quilibrated bilayer and one with the peptide of interest. How can I create a system with three copies of the peptide at a distance of 20 angstrons of the bilayer (no matter which layer), in a box structure?
Noora Azadvari
You can restrict it be above 20.0 and below 21.0 planes (relative to the bilayer)
From Packmol:
The planes are defined by the general equation ax+by+cz−d=0 and it is possible to restrict atoms to be above or below the plane. The syntax is:
above plane a b c d
below plane a b c d
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