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Article ID: 909 - Last Modified: December 4, 2013

How can I embed a G-protein coupled receptor (GPCR) in a membrane for a Desmond MD simulation?

You can run the script mold_gpcr_membrane.py with the following command:

$SCHRODINGER/run mold_gpcr_membrane.py prepared-gpcr-protein -lipid lipid -j jobname

where prepared-gpcr-protein is the GPCR structure, which must be prepared using the Protein Preparation Wizard, and lipid can be dppc or popc. The protein-membrane system is written to the file jobname-out.cms. The script aligns the input protein to a pre-equilibrated protein_membrane system, wherein the boundary box size is calculated using the default buffer distance of 10Å.

This script is included in software distributions that have been purchased from Schrödinger.

Keywords: mold, equilibration, molecular dynamics

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