Re: CCL:G98: ONIOM and Amber on TM systems

["Stefan Fau" <fau |-at-| qtp.ufl.edu>]

Hi Valentine,
 The ONIOM method requires 3 calculations for
 a molecule: a low level calc of the whole molecule
 (ll/all), a low level calc of the high level part (ll/part)
 and a high level calc of the high level part (hl/part).
 The ONIOM energy is defined as
 E(ONIOM) = E(ll/all) - E(ll/part) + E(hl/part)
 Although the low level energy contributions of the
 high level part seem to cancel out, that is not
 completely true. In order to have well behaved
 high level parts, broken bonds are saturated with
 hydrogen. This causes a difference in the MM
 energy terms between ll/all and ll/part that reaches
 at least three atoms inside the high level part
 (dihedral angle with the saturation H). For that
 reason (and programming reasons, I assume),
 you need MM parameters for all atoms in the
 molecule.
 In the last few days there was a thread concerning
 ONIOM energies. One of the mails pointed to an
 article that explains the ONIOM method in more
 detail.
 Stefan
 ______________________________________________________________________
 Dr. Stefan Fau                    |      fau |-at-| qtp.ufl.edu
 Quantum Theory Project     |     (352) 392-6714
 University of Florida
 Gainesville, FL 32611-8435