How to orient the protein for lipid bilayer simulation

I was trying to perform an MD of a protein (Mrgprx2) in a lipid bilayer.

The domain of the protein looks like this:

Thus I’d like to have the transmembrane part of the protein to be buried in lipid membrane,
and the extracellular part of it to be placed outside membrane.

I was following the Gromacs Membrane Protein Tutorial.

However the protein orientation I get is not as I expected.

Notice that the whole protein is buried in the lipid and in tilted position instead of perpendicular with respect to the lipid bilayer.
How can I properly orient the protein in the membrane?

G.V.

One way to do this is by VMD. You can rotate the protein (first select it) and manually change the orientation until it satisfies your needs (though this is off-topic about Gromacs). You can find many online resources of VMD to achieve that.

1 Like

@nano Thank you. I follow your advice. I used VMD to re-orient the protein in combination with editconf rotation:

gmx editconf -f myprotein_processed.gro -rotate 0 90 0 -o myprotein_newbox.gro -c -box 6.41840 6.44350 6.59650

It worked.

The final result I got is this:

Thank you.
G.V.