Re: [AMBER] Fwd: tutorial for finding binding free energies

From: David Case <>
Date: Fri, 13 Sep 2019 21:39:00 +0000

On Fri, Sep 13, 2019, Sadaf Rani wrote:

>Could you please suggest a tutorial in amber for finding binding free
>energies of more than one ligand in a complex....

Do you mean a receptor that binds two ligands at the same time? Can you
be specific about exactly which "binding free energy" you wish to
estimate (since with multiple ligands, there are multiple binding

If I am not misunderstanding your question, you would probably want to
estimate each binding event individually: that is, you need to estimate
the free energy differences between four states (R, RL, RL' and RLL',
where R=receptor and L,L' are two ligands).

To get from R to RLL', you go through intermediate states with just one
ligand bound.


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Received on Fri Sep 13 2019 - 15:00:03 PDT
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