Re: [AMBER] How to add restraints to a ligand correctly while decoupling it from complex?

From: Jason Swails <>
Date: Tue, 3 Nov 2015 09:14:57 -0500

On Mon, Nov 2, 2015 at 7:56 AM, wliu <> wrote:

> Dear all,
> I am trying to use double decoupling method to calculate absolute
> binding free energy of a protein-ligand complex. According to this
> method, ligand need to be decoupled from solvent and complex
> respectively. I have already decoupled the ligand from solvent. After
> that, I want to decouple the restrained ligand from complex using
> Thermodynamic Integration in Amber. To keep ligand from moving out while
> decoupling, restraints should be add on it correctly. So any advice?
> Have someone done this before?

​What I would do is define an NMR flat-well distance restraint between the
center of mass of the ligand and the "center" of the binding pocket, and
turning "on" the restraint at a distance that is large enough to encompass
the entire binding pocket (so that the ligand can explore the whole thing
during all phases of the simulation). You can do this via the flat-well
potential fairly easily, making sure that the force constant rk1 (at small
distances) is 0 so as to not penalize the ligand being inside the active
site, and then setting r3 (the distance at which the potential is turned
*on* in a quadratic form) to the distance large enough to encompass the
binding pocket.

A sample restraint file might look something like this (untested! this is
just to give you an example of what to look for in chapter 24 of the Amber
reference manual):

   iat=-1, -1, igr1=100,101,102,103,104, igr2=200,201,202,203,204,
   rk1=0, rk2=20.0, r1=0, r2=0, r3=10, r4=20,

This defines a restraint between the COM of atoms 100-104 and 200-204 (your
"active site" and "ligand atoms", respectively), with no penalty until that
distance increases to 10 A, and a 20 kcal/mol/A^2 force constant beginning
at 10A.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Nov 03 2015 - 06:30:03 PST
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