ffTK and phase angles

From: Benjamin Hill (ben.luc.chem_at_gmail.com)
Date: Thu Jun 19 2014 - 17:43:28 CDT

I have a question that regards the generation of CHARMM parameters using
the "force field tool kit" (or ffTK) plugin in VMD. This fixes dihedral
phase angles to either 0* or 180*. Doing so allows the results to be
compatible with the "CHARMM-general force field", or CGenFF

I have a question regarding the parameterization of a pyruvate-like
molecule, which (like pyruvate) is very acidic. Pyruvate is frequently
drawn with with the carbonyl group // carboxyl group all drawn in a flat
plane. Since it is planar, an energy minimum is seen when the dihedral
angle regarding
[ "carboxyl Oxygen" - "C" - "C" - "carbonyl Oxygen" ]
is set at 0*. Thus, (as I understand) this dihedral phase is set at 180*.

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? If so, can the ffTK be manipulated so that this is not
forced, and instead can give other angles? I understand that this would
make the results incompatible with the CGenFF, but it would otherwise be ok
CHARMM simulations.

Diolch i chi,

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:31 CST