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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 space for them between LPS (lipopolisacharides) pushing LPS-s to the edges of simulation box.

If I use only one peptide, it is not problem, empty space is not big, and CHARMM-GUI successfully finishes job. But when using more peptides, empty space created underneath them is large, so LPS-s are pushed to the edges, tightly packed, which obviously causes problem for CHARMM-GUI and gives 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.

I report error to CHARMM-GUI developers, and got short answer:

View step3_packing.pdb.

I looked, and see nothing strange, nothing to lead me to solve the problem.

Any idea where to look, or how to solve problem?

hole_between_LPSs_picture1 hole_between_LPSs_picture2

p.s. This question is appropriate for CHARMM forums, but I've not been able to register on CHARMM forums prior this question.

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  • $\begingroup$ Welcome to the site! Since they suggest that one file may be the source of the error, would you be able to include that in your question as a code block? $\endgroup$ Commented Mar 25, 2022 at 12:48
  • $\begingroup$ @Tyberius Sure, it's a relatively large file. Seems that there is no option to attach file here.. :/ $\endgroup$ Commented Mar 25, 2022 at 13:08
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    $\begingroup$ For a really large file that doesn't fit as a code block, you can upload it to GitHub. One of our users set up a repo for larger files related to questions here. $\endgroup$ Commented Mar 25, 2022 at 13:44
  • $\begingroup$ Do you need help uploading the file to GitHub? Without it, I think this question is taking up space in our unanswered queue and distracting answerers from questions which are more answerable. Is the problem that you didn't know what folder to put the file in? You can make a folder called 8851 (because that's the number in this question's URL). $\endgroup$ Commented Sep 7, 2022 at 14:16
  • $\begingroup$ This post appears to be abandoned. It can be reopened if OP addresses questions/suggestions from the comments. $\endgroup$ Commented Sep 7, 2022 at 22:40

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