Re: [AMBER] the energy between two ligand molecules

From: Jason Swails <>
Date: Fri, 15 May 2015 05:18:54 -0400

On Fri, May 15, 2015 at 5:10 AM, chemjxn <> wrote:

> Hello,
> I want to calculate the interaction energy between two ligand molecules
> such as a water molecule and a guanine molecule by using amber program. How
> can I do for such complex? I treat the two molecules as two ligand or other
> way? Please help me. Thank you!

​The only programs/methods that make a distinction between "ligand",
"receptor", and "complex" are MM-PBSA and LIE​. You can use energy
decomposition in to get a qualitative understanding of
interaction energies, or the "energy" command in cpptraj may suffice for
your needs as well (see the documentation for each to help you decide which
method will be most helpful to you).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri May 15 2015 - 02:30:18 PDT
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