Re: [AMBER] leap changes residue order

From: Ignacio Faustino <>
Date: Thu, 2 Jul 2015 18:51:58 +0200

Sorry for the delayed reply. Thanks for the suggestions.

Both ways worked. After updating AmberTools to the latest version (last
patches applied) setting the default reordering to *off* worked. Also
creating mol2/frcmod files for a "new" water residue worked. I also checked
that both topology files are the same.

Thanks for your help, especially to Jason and Hannes.

Ignacio Faustino

On 1 July 2015 at 18:14, Jason Swails <> wrote:

> 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
> > 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).
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Thu Jul 02 2015 - 10:00:05 PDT
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