Hello Tommy,

You can use this server (PPM in OPM site), https://opm.phar.umich.edu/ppm_server3_cgopm , to determine the orientation and depth of your protein in the membranes. After that, you can use the model from PPM in CHARMM-GUI.

Best,

Youngki

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Youngki You, PhD

Post Doctorate RA, Biochemical Mechanisms

Structure, Function & Design

Biological Sciences Division

Pacific Northwest National Laboratory

Tel: +1 (509) 371-6660