Subject: Re: CCL:rir in MM3

From: [email-masked] (Per-Ola Norrby)
Date: Mon, 10 Feb 1997 11:30:31 +0100

Dr. Kelterer asked:
>Dear Netters,
>I have some unclear results with MM4(94):
>By calculating a system with a 5-ring I received
>sometimes "restricted internal rotation (rir) frequencies"
>i.e. characterised lower than 40/cm. But I did no-restriced
>motion input. So, it's not clear for me what quality of this
>minimum is.
>Sometimes I got also "free internal rotation (fir) frequencies"
>i.e. 0/cm (this was after a calculation by dihedral driver option
>or from an stochastic search), and if I made little changes in one
>dihedral angle, this became a saddle point.
>But the restricted frequencies remained restricted ones.
>Can someone help me with experience or some papers?

        The terms "restricted" and "free" in the above output may be a
little confusing, they don't refer to the way the calculation was run, but
rather is a simplified diagnostic.  What it tells you is simply that you
cannot trust the thermodynamic corrections when you have "restricted
internal rotation (rir) frequencies" in the calculation.  The minimum is
good though, as long as you only want to use it for verifying stationary
points, you're OK.

        My guess is that you shouldn't use the frequency calculation with
dihedral driver (I'm using MM3(92), I thought they were incompatible).
When you are using dihedral driver, you're almost certain to end with a
structure which is not a true minimum, just a restricted one.  In this
case, the frequency analysis has no meaning.  I'm not sure if MM3(94) has
the ability to project out the forces due to the restrained dihedral (it
does seem that way if you can run it), in that case the calculation might
be good for verifying that the structure is a stationary point with respect
to the remaining degrees of freedom, but I'm on shaky ground here, I don't
really know what is allowed or not.  Anybody else?

        Per-Ola Norrby

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 *  Per-Ola Norrby, Associate Professor
 *  The Royal Danish School of Pharmacy, Dept. of Med. Chem.
 *  Universitetsparken 2, DK 2100 Copenhagen, Denmark
 *  tel. +45-35376777-506, +45-35370850    fax +45-35372209
 *  Internet: [email-masked], http://compchem.dfh.dk/

---

From: Andy Dustman <[email-masked]>
Date: Mon, 10 Feb 1997 13:23:30 -0500 (EST)

> really know what is allowed or not.  Anybody else?

When you use the dihedral driver, you need to use block diagonal
Newton-Raphson minimization, not full Newton-Raphson. The latter mode is
necessary for vibrational calculations. You can, however, use the torsion
driver to drive over an energy barrier and THEN use full Newton-Raphson on
that conformation to find a transition state. 

--
Andy Dustman / Computational Center for Molecular Structure and Design / UGA
You can have my PGP public key by sending mail with subject "send file key".
You can have my PGP secret key when you pry it out of my cold, dead neurons.
http://charon.chem.uga.edu/~andy    mailto:[email-masked]    <}+++<