Thanks for the source David! I'll take a look through it.
I'm no expert either in seQM/MM either, but as I understand it, because
AM1/PM3/etc make heavy use of MNDO/NDDO/etc approximations, one again needs
to adjust the integrals involved in the hcore term for seQM/MM. See for
instance the paper here (
https://onlinelibrary.wiley.com/doi/10.1002/jcc.540110605) and the
discussion around Eq 10-14.
I'm unclear if this is the main way seQM/MM couplings are computed or if
there are other popular schemes. For instance, MOPAC uses a different
scheme (
http://openmopac.net/manual/QMMM.html), with the paper detailing
this implementation here (
https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.540130212 - see
discussion for eqs 1-5).
So my question could be re-phrased as: Do you know if AMBER's sander
follows either of the above schemes or perhaps just uses a canonical seQM
1/r_qm evaluation for h_core?
Alan Chien | Senior Scientist II
*he/him/his*
[image: Schrödinger, Inc.] <https://schrodinger.com/>
On Wed, May 24, 2023 at 9:46 AM David A Case via AMBER <amber.ambermd.org>
wrote:
> >On Tue, May 23, 2023, Alan Chien via AMBER wrote:
> >
> >I'm trying to determine the details of the QMMM coupling scheme used in
> the
> >sander module when doing semi-empirical (PM6, AM1, etc) calculations.
> >Specifically, the manual doesn't detail the form of h_core in equation
> >10.3.
>
> Sorry: I didn't read your email carefully enough, and answered too soon.
> You did make clear that you were looking at Eq. 10.3 in the Reference
> Manual.
>
> I think h_core in Eq. 10.3 is just 1/r_qm. That is, one just has the
> Coulomb interaction between Q_m, the charge on MM atom "m", and Z_q, which
> is the nuclear charge minus the core charge on QM atom "q".
>
> ...hope this helps....dac
>
>
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Received on Wed May 24 2023 - 10:30:02 PDT
