How to orient the protein for lipid bilayer simulation in Gromacs

Question

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.

Answer 1

In the Step One: Prepare the Topology, second paragraph, you can find the following information:

The peptide was prepared in-house using the xLeap module of AmberTools, using ideal backbone geometry of an α-helix (φ = -60°, ψ = -40°). The .pdb file was oriented along the z-axis using editconf -princ, followed by a rotation about the y axis. Note that in GROMACS-3.3.x, the -princ option oriented the long axis of the structure (in this case, the helix axis) along the z-axis by default, but this option has changed as of GROMACS-4.0.4, which orients the long axis along the x-axis. If you want to skip the construction of this peptide, the properly oriented structure can be found here.

I think that before setting up your system, you can prepare (rotate) your protein and use it in the orientation you want.

Answer 2

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: