RE: AMBER: about QMMM output

From: Ross Walker <ross.rosswalker.co.uk>
Date: Fri, 4 Jul 2008 09:30:09 -0700

Just to clarify some more here.

The ESCF printed, for a QM/MM PME calculation, in the sander output file is:

ESCF=E(QM)+E(QM/MM)ElecRS

Where ElecRS refers to the real space QM/MM electrostatic interaction, i.e.
what is inside the cut off, adjusted for Erfc. Note that E(QM/MM)VDW is
calculated classically and so this gets included in the general VDWaals
energy term.

The QM/MM PME part of the electrostatics ends up in EELEC with the rest of
the PME and MM/MM real space interactions.

Gustavo is right that there are also certain covalent terms crossing the
QM/MM boundary and they end up in the corresponding BOND, ANGLE etc terms.
However, in your case the contributions would be zero here.

I hope this helps, the papers Gustavo refers to will hopefully make it
clear.

All the best
Ross

> -----Original Message-----
> From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
> Of Gustavo Seabra
> Sent: Friday, July 04, 2008 8:33 AM
> To: amber.scripps.edu
> Subject: Re: AMBER: about QMMM output
>
> Yes and no ;-)
>
> That is the SCF energy, the energy from the QM calculation. This
> energy is influenced by the presence of the MM atoms, so in a way you
> can say it does include /some/ of the QM/MM electrostatic interaction
> energy. However, the QM/MM interaction also has other terms, like van
> der Waals and bond terms, which are not included there.
>
> For more details, see:
> J. Phys. Chem. A (2007), 111, 5655-5664
> J Comput Chem (2008), 29 10191031
>
> HTH,
> Gustavo.
>
> On Thu, Jul 3, 2008 at 10:40 PM, linfu <linfu3200.mail.sioc.ac.cn> wrote:
> > Dear AMBER community!
> >
> > I have question about QMMM output. for example QM part use PM3
> > In the output there is a energy term called PM3ESCF.
> > Does PM3ESCF(ligand) = E<QM(ligand)>+E<QM(ligand)/MM(water+protein)> ?
> > if the ligand has no covalent bond with protein and QM part is ligand.
> >
> > Thank you in advance!
> >
> >
> > Best Regards,
> > Lin
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Received on Sun Jul 06 2008 - 06:07:48 PDT
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