Re: [AMBER] leap changes residue order

From: Jason Swails <>
Date: Wed, 1 Jul 2015 12:14:17 -0400

On Wed, Jul 1, 2015 at 12:04 PM, Ignacio Faustino <> wrote:

> Dear AMBER users,
> I want to calculate the free energy associated to Na+ binding using TI. I
> would like to transform it into a water molecule while at the same time
> transforming a water molecule in the bulk by another Na+ to keep the
> neutrality. I try to create two topology files for both ending states (I
> have only AMBER12) but Leap keeps on changing the residue order. There is
> no problem when creating the initial state (Na+ in the binding site and WAT
> in the bulk, Na+ appears before WAT in the input pdb file) but if I edit
> the pdb to create the final state (WAT in the binding site and Na+ in the
> bulk, this time WAT residue appears before Na+) then Leap changes the
> residue order. It seems like it puts all Na+ ions first and then the water
> molecules without taking into account the input order from the pdb file.

​Yes, this is intentional. In several places, Amber makes the assumption
that all solvent residues appear at the very end of the system, which
allows solvent residues to be "identified" using a single number.

AmberTools 15 introduced a new command in tleap that allows you to disable
this behavior, but buyer beware. I don't know how many places depend on
the water residues coming last, so I don't know what you will break by
using this. But the following command should do the trick:

set default reorder_residues off

Note, this will *only* work in AmberTools 15, so you need to download that
version (the prmtop file can still be used with Amber 12).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Jul 01 2015 - 09:30:05 PDT
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