Re: [AMBER] Concerning nonbonded exclusions and MMPBSA

From: Aron Broom <>
Date: Thu, 18 Oct 2012 12:35:24 -0400

Hi Jason,

Thanks so much for the detailed reply. That makes complete sense now.


On Thu, Oct 18, 2012 at 11:57 AM, Jason Swails <>wrote:

> On Thu, Oct 18, 2012 at 11:45 AM, Aron Broom <> wrote:
> > Hello AMBER users,
> >
> > I'm wondering about how nonbonded exclusions are treated in MMPBSA. Are
> > they included just as in a normal MD run in AMBER?
> >
> > The reason I ask is that I'm somewhat confused about these exclusions. I
> > had written my own little code to calculate just the electrostatic
> > potential energy portion of something in order to do part of an MMPBSA
> > style calculation (for reasons that are too uninteresting to go into, it
> is
> > infeasible for me to use MMPBSA or AMBER for this beyond testing
> > purposes). I was confused that my numbers were coming out differently
> from
> > those reported in a normal AMBER run, and tracked the problem to the fact
> > that I was calculating all the pairwise interactions, and while I had the
> > AMBER cutoff at 999 angstroms, there are still the 1-2, 1-3 complete
> > exclusions and the 1-4 scaled exclusions. I had thought these exclusions
> > were just there to save computational power because those interactions
> were
> > weak compared to the bond, angle, and dihedral components that would also
> > affect those atoms.
> >
> No, actually these interactions would be incredibly large since the
> distances are so short. They are neglected because the bond and angle
> terms are parametrized to account for the full bonded interaction. The
> added cost of calculating these exclusions would be next to nothing (since
> the exclusion list is so small compared to the full pair-list), so it is
> excluded because that is the *actual* definition of the force field.
> The way Amber handles this is to set up an "exclusion" list in which each
> atom contains a list of atoms in which nonbonded interactions should *not*
> be calculated. This is listed in the topology file (NUMBER_EXCLUDED_ATOMS
> and EXCLUDED_ATOMS_LIST). The list includes all bonded, angled, and
> dihedral-ed atoms; all of which are excluded from the core nonbonded
> calculation. The 1-4 interactions are added back in as a sum over unique,
> proper dihedrals, after which they are appropriately scaled.
> The GB routines take this exclusion list directly from the topology file
> (which means you can edit that to add your own exclusion rules via ParmEd
> or something), but the PME routines rebuild the exclusion list based on the
> system topology.
> So anyway, my question basically is: if one wants to calculate the actual
> > electrostatic potential energy of a protein for instance, is ignoring
> those
> > exclusions accurate, or should they really be included in order to get
> > accurate results? And then, does MMPBSA include them?
> >
> They must be included to get accurate results. And yes, MMPBSA includes
> them. MMPBSA does not actually compute energies directly, it calls
> external programs to do so (either a NAB program or sander). All external
> programs that 'correctly' implement the Amber force field implements these
> exclusions.
> HTH,
> Jason
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
AMBER mailing list
Received on Thu Oct 18 2012 - 10:00:03 PDT
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