Knowledge Base

How can I calculate relative binding energies of protein-protein complexes?

This can be done using Prime MM-GBSA. A warning is displayed about the ligand having more than 300 atoms when you start the job from the GUI. However, this is just a warning, and does not stop the calculation from starting.

Keep in mind that the dG_bind energies calculated by Prime MM-GBSA do not necessarily reflect the actual free energy of binding, as explained in Article 1647.

To ask a question or get help, please submit a support ticket or email us at help@schrodinger.com.

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