Re: [AMBER] QM/MM energy

From: Jason Swails <>
Date: Sat, 1 Jan 2011 22:52:03 -0700


On Sat, Jan 1, 2011 at 9:03 PM, Eliac Brown <> wrote:

> Dear AMBER
> I am calculating the QM/MM-GBSA binding energy. The QM region covers the
> ligand and few residues of the protein.
> The energy terms is some way confused. One recent email post here discusses
> the energy components.
> I have two questions:
> Firstly, why QM-MM van der waals interactions are included in VDWALLS
> classically? what the reason behind it? I read many papers showed
> semi-empirical methods could estimate van dar waals interaction in a good
> agreement with ab initio methods.

But in the case of QM-MM interactions, both atoms are NOT treated quantum
mechanically, so a quantum mechanical treatment (even semi-empirical) of the
dispersion interactions doesn't make any sense. The easiest approach is to
just give the quantum atoms classical VDW parameters when calculating
non-bonded interactions between QM and MM atoms (just like QM atoms are
given classical partial charges based on some sort of charge derivation
scheme). Hence, this is a classical mechanical contribution and belongs
most appropriately in VDWAALS if we don't create another field for these
terms (i.e. QMMMVDW or something).

The second question is that I calculated the energies of the ligand,
> receptor and the complex using QM/MM method. I used the conventional
> equation of calculating the binding energy:
> EEL+AM1ESCF+ESURF)receptor
> Sure, in case of ligand, BOND+ANGLE+DIHED+VDWAALS will be zero.
> I am just afraid to miss something. is that all or should I pay attention
> to something else?

What are you treating with quantum here? Why is BOND + ANGLE + DIHED +
VDWAALS equal to zero in this case? If the whole ligand is QM, then I
agree. However, EEL and the 1-4 terms should also be zero I imagine, as you
will only have a quantum mechanical energy and solvation energy for a system
treated entirely with QM (AM1ESCF, EGB, and ESURF). Perhaps EEL will be
non-zero based on the way the GB is handled, I'm not quite sure how the
bookkeeping is done. Perhaps others can comment more thoroughly.

Good luck,

> Eliac
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Sat Jan 01 2011 - 22:00:04 PST
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