Re: [AMBER] seek for how to calculate the binding free energy of a covalent inhibitor

From: David A Case <>
Date: Tue, 17 Sep 2019 15:20:30 -0400

On Tue, Sep 17, 2019, 石娜 wrote:
> I know how to compute the binding freeenergy of the ligand and protein
> whenthe ligand does not bond to the protein. But, how to calculate the
> binding freeenergy of a covalent inhibitor in amber. Could you please help
> me to solve themout? Thank you very much. I am looking forward for your
> answers.

Amber has no general way to deal with this, since the strength of the
covalent bond being created is key to the binding affinity, yet is not
represented in force field calculations.


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Received on Tue Sep 17 2019 - 12:30:02 PDT
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