Hello, first time here
I'm trying to build outer membrane of E. coli with small peptides above it, with CHARMM-gui.
Peptides should be positioned above
the membrane but charmm-gui creates empty space (obviously for them) between LPS (lipopolisacharides) pushing LPS-s to the edges of simulation box (see attached pictures 1 and 2).
If I use only one peptide, it is not problem, empty space is not so big, and charmm-gui sucessfully finishes job. But when I use more peptides, empty space created underneath them is large, so LPS-s are pushed to the edges, tightly packed, which obviously causes problem, and process terminates with error:
"Charmm terminates abnormally. Please check the output or report this failure to the CHARMM-GUI developers. The bilayer generation is stopped to prevent an infinite loop. Please refresh the browser to restart the bilayer generation with different random seed."
I tried several times with the same outcome. It looks like membrane builder thinks that peptides are "inserted" in LPS, so it leaves empty space for them in between LPS-s.
To exclude possibility that peptides overlaps with LPS, I use "translate protein" to z=110 A (while keeping membrane small, ~80A , see picture "outer_membrane.png")
I report error to charmm-gui developers, and got short answer: "View “step3_packing.pdb”. "
I looked at that file (attached with .txt extension), and see nothing strange, nothing to lead me to solve the problem, just ordinary koordinates of (orange) beeds (see picture 2 and 1 ) which should be later substituted with LPS-s and lipids.
Any idea where to look, or how to solve the problem?
I appreciate time and consideration..