Hello,
On Sat, Jan 1, 2011 at 9:03 PM, Eliac Brown <eliacbrown.yahoo.com> 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:
>
> dG=(BOND+ANGLE+DIHED+VDWAALS+EEL+EGB+1-4 VDW+1-4 EEL+AM1ESCF+ESURF)complex
> -(BOND+ANGLE+DIHED+VDWAALS+EEL+EGB+1-4 VDW+1-4
> EEL+AM1ESCF+ESURF)ligand-(BOND+ANGLE+DIHED+VDWAALS+EEL+EGB+1-4 VDW+1-4
> 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,
Jason
Thanks
> Eliac
>
>
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sat Jan 01 2011 - 22:00:04 PST
