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A.3.2 RTOPH6

The changes that have been made to date are the inclusion of two additional improper dihedrals spanning the rings of tryptophan to distribute the out of plane bending forces more evenly. When used with the PARAM1 parameters, see PARAM1, this gives a correct out of plane skeletal vibration for tryptophan at between 400 and 500 cm-1 with relatively few high frequency modes induced by coupling of improper dihedral terms.

A second change is the repair of an error in the angles of the heme residue. Two angles were transposed in the second and third atoms resulting in incorrect specification of the desired angle. The old angles were 6-9-10 and 3-9-10. The correct angles are 6-10-9 and 3-10-9. This change results in a lower angle energy for the heme, but little change in geometry.

A third set of changes have been made in the builder information sections of the aromatic rings. The dihedral angle values have been set so that more or less correct rings will be built (the old values would result in figure eights and other such oddities).