The accuracy of native structures, X-ray and NMR, can be increased by performing a limited geometry optimization, starting with the conditioned native structure.
The optimized geometry is a hybrid of the PM6 geometry, assuming that PM6 is used, and the native geometry. The hybrid heat of formation, H', is given as:
H' = DHf(PM6) + cS(Xi - Xi(0))2
That is, at each geometry, a restraining potential is added to the PM6 heat of formation. The proportionality constant "c" is 3 kcal/mol/Å2.
The effect of the restraining potential is to reduce PM6 errors in the secondary, tertiary, and quaternary structures. It has very little effect on the primary structure, e.g., bond lengths and angles.
The effect of the restraining potential can be illustrated using crambin, 1CBN. The difference in heat of formation of crambin, after preconditioning (optimizing the positions of the hydrogen atoms), and after complete geometry optimization, is ~360 kcal mol-1. The RMS change in geometry is about 0.7 Ångstroms. If the geometry is optimized using GEO_REF, then the heat of formation drops by ~310 kcal mol-1, and the RMS geometry change is ~0.1 Ångstroms. That is, by allowing the X-ray geometry to change by 0.1 Ångstroms, about 86% of the strain energy in the X-ray structure is removed. Put another way, the resulting geometry is seven times more accurate, in terms of chemistry, than the X-ray structure.
"text" is the complete path to the reference X-ray geometry. A Windows example would be GEO_REF="M:\data_sets\CRAMBIN_1CBN_X-ray.mop", a Linux, Unix, and Mac example would be GEO_REF="/Users/jstewart/data_sets/CRAMBIN_1CBN_X-ray.mop" To change the proportionality constant from 3, put the new value after the reference data set, e.g., if a value of 10 is wanted, use: GEO_REF="M:\data_sets\CRAMBIN_1CBN_X-ray.mop"10 or GEO_REF="/Users/jstewart/data_sets/CRAMBIN_1CBN_X-ray.mop"10
GEO_REF can also be used for moving a reactant or product geometry in the direction of the transition state. Consider two data sets, reactant.mop and product.mop in folder M:\, in which the heat of formation of the optimized product geometry is lower than that of the optimized reactant geometry. The product geometry geometry can be moved in the direction of the transition state by using keyword GEO_REF="M:\reactant.mop" The .arc file can then be edited to give a new data set, product_on_slope.mop. The reactant geometry can then be moved in the direction of this new geometry by using keyword GEO_REF="M:\product_on_slope.mop" Again, edit the .arc file to give reactant_on_slope.mop. Why was the product moved first? Because by moving it towards the reactant geometry, its heat of formation would rise in proportion to the distance to the reactant geometry. When the reactant geometry is moved towards the product geometry on the slope, the distance from the starting reactant geometry to the product geometry on the slope is less, so the rise in energy would be less.
If keyword TS is present in a GEO_REF calculation, the optimization is not run. Instead, the two geometries are averaged, and the result written to a new file <file>.new.
For the current exercise, a good approximation to the transition state can then be generated from the data set reactant_on_slope.mop by using keywords TS and GEO_REF="M:\product_on_slope.mop"