GROMACS version: 2023.2
GROMACS modification: Yes/No
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Hi, I want to approximate binding energies for the docked complexes. However, the protein is a membrane protein. Can I still use gmx lie or other methods provided by GROMACS? I want just to approximate binding energies with a significant accuracy compared to the binding energies given by the docking software.
Thanks.
May be gmx_MMPBSA tool (must be installed separately) is helpful in your case? Here are instructions for installation and examples for different types of systems. Examples - gmx_MMPBSA Documentation