Re: [AMBER] Bug in LIE action command of cpptraj?

From: Jason Swails <>
Date: Wed, 27 May 2015 16:44:30 -0400

On Wed, May 27, 2015 at 4:07 PM, Samuel Bowerman <> wrote:

> Hi Jason,
> Thanks for the response. Perhaps you could enlighten me as to what part of
> the calculation is inherently explicit? For example, if I want to analyze
> the specific interaction of a ligand with a small subsection of the binding
> protein, I define two groups: "ligand" and "subset (surroundings)". How
> does explicit vs implicit matter for this case if I am only calculating
> pair-wise point-charge energies for these groups? If I were to define only
> the ligand group, then the surroundings would include the explicit waters,
> but that may not always be the case, correct?

​As I understand it, LIE is usually a difference between ligands
interacting in different environments -- the solvated protein and in
solution surrounded by water molecules. So you usually run two different
explicit solvent simulations - one of the isolated ligand in solution and
one of the ligand in its protein environment ​(in solution), and the
difference is scaled linearly, usually with separate scaling factors for
electrostatics and van der Waals.

You may be able to apply this approach in an implicit solvent environment,
but that would require GB or something of the like -- a simple dielectric
scaling isn't going to do the same thing.

All the best,
Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed May 27 2015 - 14:00:02 PDT
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