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

Matter Modeling Asked on December 20, 2021

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.
  fixed 0. 0. 0. 0. 0. 0.
end structure

structure 6vxx.pdb
  number 1
  inside box -44. 50. 0. 100. 200. 150.
  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?

One Answer

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.

Answered by Susi Lehtola on December 20, 2021

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