# Why am I losing bonds when I use PACKMOL on two proteins?

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?

• packmol is not designed to fix proteins together as far as I know. Jul 24 '20 at 2:32
• It is used to build and pack atoms and molecules. But even if it isn't proteins, the bonding is lost!! Jul 24 '20 at 2:33
• @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. Jul 25 '20 at 0:46
• The bonds are visualized in accordance with the set-up of each visualization software. Did you try other software like Chimera, for example?
– Camps
Jul 25 '20 at 1:08
• 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)
– Camps
Jul 25 '20 at 1:16