Conventional semiempirical methods use matrix algebra methods, most of which scale as the third power of the number of atoms. A consequence of this is that modeling of systems of more than 1,000 atoms is impractical.

By using Localized Molecular Orbitals (LMO), the Self-Consistent Field equations can be solved in a time proportional to the size of the system. Increasing the speed of the SCF moved the slow step to other parts of the calculation, so changes were made to all the remaining time-consuming steps to make them more efficient. Changes were also made that reduced the memory demand. The result of all these changes is that routine modeling operations can now be carried out on over 90% of all the entries in the Protein Data Bank (PDB), previously only about 10% of all entries could be used.

Most of the common modeling functions have been enhanced by the MOZYME function, these include:

• Single-point calculations.

A general impression of the change in behavior can be obtained by comparing the resources required for various single-point, i.e., single SCF, calculations. Other operations, such as geometry optimization, consist of repeated SCF calculations. All calculations shown here were done using a Windows XP Pro computer with a 4000+ or 2.41 GHz Athlon processor.

The test systems used here were constructed from a single large protein, cut into pieces of the appropriate size.

Comparison of MOPAC and MOZYME computer resources required for a 1SCF calculation

1: Numbers in parentheses are estimated

After the first SCF calculation is done, all subsequent SCF calculations run much faster:

• Geometry optimization:
This includes single point, restricted, and unrestricted, for molecular assemblies and for solids.

• Transition state location.
This operation runs at about half the speed of geometry optimization.

• Transition state refinement.
This operation runs at about 20% of the speed of geometry optimization.

• Transition state characterization.
The FORCE calculation is a rapid operation now, running in a small fraction of the time required for geometry optimization.

• Intrinsic Reaction Coordinate.
Unlike the other operations, this is very time consuming, taking 10 – 50 times longer than a geometry optimization.

• Reaction paths, grids, etc.
These can be run using only the atoms of interest, in which case it is very fast, or using all atoms at every step, in which case it is slow. The time for each point is only slightly less than a geometry optimization.

Properties of proteins (structure, energetics, reactions, etc.) are reproduced with good accuracy using PM7. For details of PM7, see: http://link.springer.com/article/10.1007%2Fs00894-012-1667-x

For accuracy of PM7 compared to other methods, see:

For accuracy of modeling protein properties, see: HTTP<add URL here>

Limitations

The current MOZYME function is restricted to closed-shell systems for which a Lewis structure can be generated. Only Restricted Hartree Fock methods can be used, ROHF and UHF are not available. This means that well-known radicals, such as ethyl, C₂H₅·, and triphenylmethyl, (C₆H₅)₃C·, cannot be modeled. An exception to this rule concerns biomolecules that contain transition metals. These are normally treated as open-shell systems, but if the main focus of interest is on geometries and energetics, they can be modeled using closed shell methods.

• Re-define chains and residue numbers

• Resequence. When hydrogen atoms are added, they are usually put at the end of the data set. This results in a non-standard PDB format. The standard PDB format can be generated using RESEQ. This puts all atoms in the same residue together. If two geometries, from entirely different PDB files are compared, the atoms in each file must first be put into the same sequence, so that there is an exact one-to-one correspondence. Unavoidable ambiguities in the PDB format definition require some extra re-arranging of atoms to ensure maximum coincidence. This is done using keyword GEO_REF.

Because the issues involved in manipulating proteins are very different from those involving small molecules, all users are strongly recommended to spend some time familiarizing themselves with the MOZYME utilities.

Preconceived ideas of charge are often wildly inaccurate. These include generalizations such as "all acid functions should be ionized" and "all arginine residues should be protonated." If these ideas were implemented, the resulting net charge on a protein would likely be nonsense.

This policy of requiring the initial structure to be uncharged might appear to be restrictive, but during a geometry optimization salt bridges will often form spontaneously, so the initial uncharged species is quickly replaced by a more realistic system. After the geometry is optimized, any ions the user considers important can then be added. If the entire protein has to have a certain net charge, protons can be added or removed as necessary. Thus bacteriorhodopsin would have the retinal Schiff base nitrogen atom protonated to give bR⁺.

The end result is a well-defined protein with the correct charged sites.

• Check hetero groups. Most utilities that add hydrogen atoms do a good job of handling the common residues, but a poorer job with hetero systems, such as the heme group. Because of this, almost all the errors in adding hydrogen atoms occur with hetero groups. Therefore, these groups should be checked carefully to verify that the degree of saturation is correct.

• Identify and characterize uncommon residues. If a residue is not recognized by MOPAC, check that it is correct. If it should be one of the 20 common residues, either add the missing atoms, or use XENO to allow the residue to be recognized. If it is a modified residue, such as the retinal group in bR, use XENO to re-define it as the parent residue  Do not ignore unrecognized residues – they usually indicate a fault in the data set.

• Trust that the charged sites printed are correct. The method for calculating charged sites is very robust. If it says that a site is charged, believe it. In older versions of MOPAC, charged sites were not printed, and about twenty users reported errors in MOPAC, saying that the net charge it wanted was incorrect. In every case, errors were found in the user’s data set, due to simple errors in assigning hydrogen atoms.

  Although the charges reported by MOPAC are always correct, minor problems might be encountered in extended, delocalized,