From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Thu Jun 19 2014 - 20:01:05 CDT
On 06/19/2014 06:43 PM, Benjamin Hill wrote:
> However, this only applies to the protonated form of pyruvate-- based on
> MP2/6-31+G* optimizations, the anion is far from planar. For this
> dihedral, an energy minimum is now seen at, very approximately, 30*.
>
> Would the forcing of the phase angle to be either 0* or 180* be
> detrimental in this case? (...) I understand that this
> would make the results incompatible with the CGenFF
I sometimes wonder why I spend time maintaining this FAQ...
http://mackerell.umaryland.edu/~kenno/cgenff/faq.html#phase
To put it differently, most molecules have more than one (local) minimum
energy conformation. Since pyruvate is achiral, there *must necessarily*
exist another minimum energy conformation that is the mirror image of the
one you found, with all dihedrals having the opposite sign, and with an
energy that *must necessarily* be exactly the same. In order for the
mirror-image conformation to have the same energy, all dihedral phases
*must necessarily* be 0 or 180. CGenFF compatibility has nothing to do
with this; it is a matter of adherence to basic symmetry. Using other
phases for this molecule would be flat-out unphysical, regardless of the
force field.
Also note that restricting the phases to 0 or 180 does not necessarily
favor flat conformations. The *only* thing it does is enforce a symmetric
potential.
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