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Article ID: 121 - Last Modified: May 4, 2011

During relative binding FEP, I am getting a very high dE energy for a lambda window. Why is this?

There can be multiple reasons for this, and it depends on the size of the mutation and location in the binding pocket. For example, H→Phe in a solvent-exposed pocket may be easy to do compared to a buried pocket. The default lambda window schedule may not be optimum, and you can customize your lambda schedule either by using the FEP GUI or modifying the config file (.cfg).

Keywords: Desmond, FEP, customizing lambda window

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