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

From: Ahmed Elrashedy <>
Date: Tue, 17 Sep 2019 14:46:57 +0200

Dear Shi

it is the same as ligand -prtein interaction , all of what you need to musk
the covalent ligand number when you run ant-MMGPSA and it will run with

Thank you and Best regards.


Research Assistant

Molecular Bio-computation and Drug Design Laboratory

Discipline of Pharmaceutical Sciences

School of Health Science

University of KwaZulu-Natal

Westville Campus

Private Bag X54001

Durban 4000

South Africa

On Tue, Sep 17, 2019 at 2:22 PM 石娜 <> wrote:

> Hi拢潞
> 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.
> Yours sincerely!
> Na Shi
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Received on Tue Sep 17 2019 - 06:00:03 PDT
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