Great! If in Amber's mechanical embedding QM/MM approach reported SCF energy
includes *only* electrostatic influence of "non-QM" atoms on "QM" atoms
(with Ewald summation included and all bonded and non-bonded contributions
of "non-QM" atoms are exactly zero), that would be perfect. Does anyone know
which flag(s) should be turned on for a such single point run ('independent'
of Amber's QM/MM dynamics)?
In case of using "NTR" keyword there is additional contribution to total
energy - RESTRAINT. Another option that I've tried is using *"ibelly*" mask,
allowing only "QM" atoms to move. This helped in sense that all bonded
contributions of solvent molecules are exactly zero (I've compared bonded
contributions to energy by comparing calculations with *"ibelly*" keyword on
and only "QM" subsystem in gas phase). But, non-bonding interactions of
"non-QM" atoms remain sofar as unsolved problem to me.
Best regards,
Jura
2011/4/12 Gustavo Seabra <gustavo.seabra.gmail.com>
> Could you describe in more detail what you want to do?
>
> In Amber's QM/MM approach, when you do a single point calculation, the
> SCF energy reported already includes the influence of "non-QM" atoms
> as point charges over the QM region. If you also turn off the periodic
> boundary conditions, that's all you get. Otherwise, an Ewald sum for
> the long range electrostatic interactions will also br included.
> Finally, you can look at the "NTR" and "NTF" options for sander to
> turn off particular terms of the force field.
>
> HTH,
> Gustavo.
>
> On Tuesday, April 12, 2011, Jurica Novak <jnovak.irb.hr> wrote:
> > Dear Amber user,
> >
> > Could anyone suggest me how to run Amber single point calculation in a
> way
> > that atoms of solvent are represented only as a point charges (with all
> > other interactions - bonding and nonbonding - turned off), while in the
> same
> > time all interactions of solute atoms are accounted for?
> >
> > Thanks in advance,
> >
> > Jura
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> --
> Gustavo Seabra
> Professor Adjunto
> Departamento de Química Fundamental
> Universidade Federal de Pernambuco
> Fone: +55-81-2126-7417
>
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>
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Received on Tue Apr 12 2011 - 07:30:02 PDT
