Membrane Protein Orientation

GROMACS version: 2021.5
GROMACS modification: Yes/No
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My membrane protein is parallel to the membrane surface, not perpendicular to the membrane (see attachments for details), how can I fix this?
The command I entered are:

  1. gmx editconf -f 1j4n_H.pdb -o conf.pdb -box 11.485 11.383 10.394
  2. gmx solvate -cp conf.pdb -cs pope.pdb -o box.pdb

Hi, editconf comes with a a “-rotate” option.

Thanks. Your suggestion looks like a charm.

You can use OPM webserver to align the protein perpendicular to the membrane.