Centering protein, ligand and lipid membrane in a water-ion box

[HoaSoup]

Hello,

I was trying to center a protein-ligand complex and lipid membrane in a box of water and ions.
I did this according to this link:

    modeller = app.PDBFile(topology_file).getTopology() # OpenMM modeller
    universe = mda.Universe(modeller, trajectory_file, in_memory=True)
    protein_and_ligand = universe.select_atoms('chainID A or chainID B or chainID C')
# chain A: protein, chain B: ligand, chain C: lipid membrane
    not_protein_or_ligand = universe.select_atoms('not chainID A and not chainID B and not chainID C')
    transforms = [mda_trans.unwrap(protein_and_ligand),
                  mda_trans.center_in_box(protein_and_ligand, wrap=True),
                  mda_trans.wrap(not_protein_or_ligand)]
    universe.trajectory.add_transformations(*transforms)
    atom_group = universe.select_atoms("all")
    centered_traj_file = trajectory_file.split(sep=".")[0] + "_centered.xtc"
    atom_group.write(centered_traj_file, frames='all')

and got this:

Centering did not work. Any help is appreciated.
Best regards,
Hoa

[orbeckst]

I probably would have tried it in the same way as you. I don't see anything immediately wrong but of course the output is not what you want. I'm sorry, I don't have an immediate solution for you. I would suggest to try it out with different components; for instance, using multiple chains for a centering operation can go very wrong if the chains are split across the box.

• Look at the options for center_in_box(). Perhaps you need wrap=True.
• You could also try the manual, step-by-step approach from the userguide: centering in the box tutorial and visualize the system after each step to see what's happening and if it's still doing the right thing; or perhaps better, build your system with the first transformation and visualize, then build with two transformations and visualize, and when this looks right, try all three transformations.
• Look at the docs for transformations

Please let us know when you find success (I am sure that others will be very interested!) or an indication that the transformations contain a bug.

[BradyAJohnston]

If you can't get it working and are able to share / link to some example data that can reproduce this error it would be good for use to be able to look into / debug. From looking at it it visually it looks like the protein has been unwrapped & centred, but the rest of the system hasn't followed so maybe it's something to do with the selections.