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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) = E (1) + E (2) - E (2)
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) = E (AM1,QM part) + E (AMBER, whole)
- 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 |