CUTOFF=n.nn

MOZYME calculations run faster when some NDDO interactions are ignored.  By default, all NDDO interactions are included between atoms separated by 9.9 Ångstroms or less, and all polarization functions between atoms separated by 10 Ångstroms or less.  For rough work, such as optimizing a structure that is far from a minimum, if CUTOFF=n.nn is used, then only point charge interactions beyond n.nn Ångstroms are used.  A suitable value for n.nn is 6.0.  This will give a large increase in speed.

If CUTOFF=6 is used, then GNORM=20 is recommended.  Once the geometry is optimized using GNORM=20, the CUTOFF should be removed, and GNORM reduced to, e.g., GNORM=10.

The effect of CUTOFF on times and accuracy of prediction of geometry can be investigated by examining the statistics for the optimization of the positions of hydrogen atoms in Crambin, a small 642 atom, 46 residue protein with formula C202H315N55O64S6, see Table I.  For a larger system, hexokinase, 2E2O, a medium-sized protein of 5717 atoms and 299 residues, C1448H3073N375O810S11, results for a 1SCF calculation are shown in Table II.  Hexokinase contains 375 molecules of water.

Table I: Crambin     Table II: Hexokinase
Cutoff Time (s) Ratio Distortion (Å) Distortion (Å) Energy (Kcal/mol) Relative
energy
    Cutoff Time (s) Ratio Energy (Kcal/mol) Relative
energy
Default 1328 1.00 49.5 0.0 -3342.2 0.0     Default 774   -45095.0 0.0
7.0 746 0.56 50.0 1.7 -3342.5 -0.3 12.0 796 -45095.0 0.0
6.0 889 0.76 49.6 1.3 -3342.1 +0.1 11.0 746 -45095.1 -0.1
5.0 599 0.45 46.3 8.8 -3334.5 +7.7 10.0 685 -45095.1 -0.1
4.0 348 0.26 51.7 5.0 -3315.8 +26.4 9.0 599 -45095.2 -0.2
3.0 119 0.09 34.9 26.7 -2952.1 +390.1 8.0 546 -45095.6 -0.4
no-opt -   0.0 49.5 -2963.6 N/A 7.0 490 -45096.7 -1.7
6.0 343 -45093.3 +1.7
5.0 309 -50783.8 -5688.8
4.0 252 -44949.3 +145.7

For the rare occasions when finer control is needed, use CUTOF1 and CUTOF2.

CUTOF1=n.nn

In MOZYME calculations, the cutoff distance for polarization functions is set by CUTOF1=n.nn. Beyond that distance, electrostatic interactions are considered only as point charges. At distances less than that given by CUTOF1, electrostatic interactions are represented by a point-charge and three polarization functions. Default: For systems of less than 30 atoms, CUTOF1 is 1000 Ångstroms; for systems of 30 or more atoms, CUTOF1 is 10 Ångstroms.

CUTOF2=n.nn

In MOZYME calculations, the cutoff distance for two-electron two center and one-electron two center integrals is set by CUTOF2=n.nn. Below that distance, the interaction between two atoms is represented by the exact NDDO approximation. Above that distance, one-electron integrals that depend on the overlap are ignored, and two-electron integrals are simplified. Instead of using all 100 two-electron integrals between two heavy atoms, only seven are used. These represent the terms <ss|ss>, <ss|sx>, <ss|sy>, <ss|sz>, <sx|ss>, <sy|ss>, and <sz|ss>.  At still greater distances, beyond CUTOF1, only the <ss|ss> term is used. Default: for systems of less than 30 atoms, CUTOF2 is 1000 Ångstroms; for systems of 30 or more atoms, CUTOF2 is 9.9 Ångstroms.