Dear
Everyone,

I
would like to thank who get me the following usefull answer to my =
question.

Original
Query:

**************

Dear
All,

i
performed a two layers ONIOM calculation (AM1:amber) on a complex
enzyme-substrate. The problem that i have is that AMBER requires all the
parameters for the ligand, even though the ligand belongs to the QM =
shell.

Is
there any ways to circonvent this problem?

Thanks
in advance.

**************

Replies:

-------------------------------------------=
--------

Dear =
Daniele,

I have never used AMBER, so maybe =
what I
am going to say is nonsense, but when running QM/MM simulations with =
CHARMM you
also have to provide parameters for the QM part, but as the program does =
not
use them, you can provide any stupid set of numbers as long as they are =
with
the correct format (they are used to create the topology file, but then =
they
are replaced). Maybe you can try this to see if it works. =
Regards,

Olalla Nieto Faza

Dpto. Quimica Organica

Universidade de
Vigo

Lagoas-Marcosende
36200 Vigo (Spain)

e-mail:
faza$at$uvigo.es

------------------------------------------------------=
-------------------------------------------

Mr. =
Bellocchi,

This is a common =
mis-understanding
with the ONIOM method. All atoms are computed at the low level, once =
with the
real system and once with just the model system which are the atoms you =
have in
the QM region. Then a =
calculation
is done with the QM method on the model system and the energy is =
computed,

E(oniom) =3D E (1) + E (2) - E =
(2)

&nbs=
p;
lo hi =
lo

where 1 is the full set of atoms =
and 2
are the atoms in the model system. hi
and lo refer to the levels of theory.

So, you do need to have =
AMBER
parameters for the ligand. =
In some
cases the contributions will cancel but not always and so Gaussian =
computes
them.

Which version of Gaussian =
are you
using? Gaussian 03 allows =
you to
supply additional parameters which can fix most of these =
cases.

Douglas J.
Fox

Technical Support

Gaussian, Inc.

-----------------------------------------------------------------

Hello =
Daniele,

As far as I am aware, the reason =
why
potentials for

the entire system would be =
required is
because of the

way ONIOM uses to calculate the =
energies
(of the QM

part of your =
system).

Briefly

E (whole) =3D E (AM1,QM part) + E =
(AMBER, whole)

&nbs=
p;
- E (AMBER, QM part)

A better explanation can be found =
in:

I.
Roggero, B. Civalleri, P. Ugliengo,
Chem. Phys.

Letts. 341 (2001) =
625-632

Plus also the original Morokuma =
papers
about ONIOM.

Hope this helps to some =
extent.

Good =
luck

Best =
Regards

Naseem

Naseem A. =
Ramsahye

Postdoctoral =
Researcher

Royal Institution of Great =
Britain

21 Albemarle Street, London, W1S =
4BS, UK

Website: www.ri.ac.uk/DFRL/N.Ramsahye

-------------------------------------------=
------------------------------

Best=
Regards

Daniele Bellocchi, PhD Student

Molecular Modeling Section

Istituto di Chimica =
e
Tecnologia del Farmaco

University
of Perugia

Italy