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I recently started using PACKMOL to pack a few proteins together. I wrote this PACKMOL code:

tolerance 3.0
filetype pdb
output E_S.pdb

structure E.pdb
  number 1
  inside box -44. 0. 0. 156. 50. 130.
  center
  fixed 0. 0. 0. 0. 0. 0.
end structure

structure 6vxx.pdb
  number 1
  inside box -44. 50. 0. 100. 200. 150.
  center
  fixed 0. 116. 0. 4.71238898 0. 0.
end structure

This code is to fix/attach one protein (SARS-CoV-2 Spike glycoprotein) onto another (SARS-CoV-2 Membrane protein) I ended up fixing different values so that the structure would look like its attached. When the code ran and the structure was generated the "Bonds" checkbox when visualized in the software OVITO was found missing meaning there is no bonding that exists.

Why did this happen?

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    $\begingroup$ packmol is not designed to fix proteins together as far as I know. $\endgroup$
    – Cody Aldaz
    Jul 24, 2020 at 2:32
  • $\begingroup$ It is used to build and pack atoms and molecules. But even if it isn't proteins, the bonding is lost!! $\endgroup$
    – SaiSmaran S B PES1201701189PES
    Jul 24, 2020 at 2:33
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    $\begingroup$ @CodyAldaz I would be grateful if you could retract your close vote now. The asker was concerned because bonds disappeared when he put 2 proteins in in PACKMOL. There is an answer saying that the user should not use PACKMOL, therefore MMSE has helped the user solve their problem. I do not want to discourage users from asking questions here, by close or downvoting them. Eventually we shall agree on our community-specific close/downvoting policies, but for now I'd be happy if downvotes aren't used & close votes are reserved for non-matter-modeling Qs, or Qs lacking detail and abandoned. $\endgroup$
    – Nike Dattani
    Jul 25, 2020 at 0:46
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    $\begingroup$ The bonds are visualized in accordance with the set-up of each visualization software. Did you try other software like Chimera, for example? $\endgroup$
    – Camps ♦
    Jul 25, 2020 at 1:08
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    $\begingroup$ I strongly recommend that you use a protein-protein docking package instead PACKMOL, as they do not only "put" the proteins together but also dock in the must favorable conformation. (a free web server you can use is HADDOCK) $\endgroup$
    – Camps ♦
    Jul 25, 2020 at 1:16

1 Answer 1

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Packmol is used to pack molecules into a given box at random positions and with random rotations.

If you want the spike glycoprotein to be attached to the membrane, you should probably prepare a new structure containing the two molecules as a single unit which Packmol won't break.

Now you have achieved your goal. Next, you can use packmol for what it's really used for i.e. adding further molecules for solvation.

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  • $\begingroup$ I haven't flagged this, but I do worry that some other people might try to flag it for conversion to a comment, especially since it fits in the comment box with even 271 more characters available. $\endgroup$
    – Nike Dattani
    Jul 24, 2020 at 15:04
  • $\begingroup$ @NikeDattani Sounds like a bug in StackExchange. $\endgroup$
    – Susi Lehtola
    Jul 24, 2020 at 16:23
  • $\begingroup$ Seems to fit: "Packmol is used to pack molecules into a given box at random positions and with random rotations. If you want the spike glycoprotein to be attached to the membrane, you should probably prepare a new structure containing the two molecules as a single unit. Then, you can use packmol for what it's really used for i.e. adding further molecules for solvation." $\endgroup$
    – Nike Dattani
    Jul 24, 2020 at 16:48
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    $\begingroup$ Or is is supposed to be a new question by itself? $\endgroup$
    – SaiSmaran S B PES1201701189PES
    Jul 25, 2020 at 3:47
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    $\begingroup$ @SaiSmaranSBPES1201701189PES This must be a separate question. You cannot expect someone that has already spent time answering one of your questions, to start answering your additional questions in comments. Every separate question should have its own separate page. $\endgroup$
    – Nike Dattani
    Jul 25, 2020 at 18:13

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