Subject: MOZYME- summary

From: Rino Ragno <[email-masked]>
Date: Wed, 1 May 1996 10:58:31 -0500 (CDT)

Some days ago I did the following question:

> 
> 
> Dear netters,
> 
> I have read about a program called MOZYME, by James J. P. Stewart and I 
> would like to try it.
> 
> Any of you out there does know anything about it?
> 
> Thank you
> 
> Rino
> 
> ++---------------------------------------------------------------------------++
> ++---------------------------------------------------------------------------++
> ||                                                                           ||
> ||  Dr. Rino Ragno                            E-mail: [email-masked]   ||
> ||  Institute for Biomedical Computing            or: [email-masked]     ||
> ||  Center for Molecular Design               Phone : 314-362-2273           ||
> ||  Box 8036, Washington University           FAX   : 314-362-0234           ||
> ||  700 South Euclid Avenue                                                  ||
> ||  St. Louis, Missouri 63110                                                ||
> ||  U. S. A.                                                                 ||
> ||                                                                           ||
> ++---------------------------------------------------------------------------++
> ++---------------------------------------------------------------------------++

Here are the answers:

>From  Edward C. Hauer
 
 Rino, here's what I found using an Altavista search for MOZYME:
  
 DONORS TO MOPAC 93
      Project MOPAC | About | This page | MOZYME | Back to Home Page | 
 DONORS TO MOPAC 93. New
      http://iti2.net/jstewart/tom.htm - size 6K - 20 Apr 96 
      http://iti2.net/jstewart/pdb.htm - size 11K - 20 Apr 96 
 
 Description of MOZYME, Version 1
      Project MOPAC: MOZYME | About | This page | MOPAC 93 | Back to Home 
 Page | Web-Page:
      HTTP://ITI2.NET/JSTEWART/ Tel: USA+(719) 488-9416 FAX: USA+(719)...
      http://iti2.net/jstewart/mozdesc.htm - size 14K - 20 Apr 96 
 
 Description of MOPAC 93
      Project MOPAC | About | This page | MOZYME | Back to Home Page | 
 Web-Page:
      HTTP://ITI2.NET/JSTEWART/ Tel: USA+(719) 488-9416 FAX: USA+(719) 

 Project MOPAC - Other Interesting Sites
      Project MOPAC - Other Interesting Sites | About | MOPAC 93 | MOZYME 
| 
 This page | Back to Home
      Page. Other Interesting Sites. Cambridge Soft has added...
      http://iti2.net/jstewart/related.htm - size 2K - 21 Apr 96 
 
 Project MOPAC - Jimmy Stewart
      Project MOPAC Jimmy Stewart | About | MOPAC 93 | MOZYME | Back to 
 Home Page | Project MOPAC
      - Jimmy Stewart. Address: Dr James J. P. Stewart, Stewart...
      http://iti2.net/jstewart/jstewart.htm - size 839 bytes - 21 Apr 96 
 
 Project MOPAC - Fujitsu
      Project MOPAC - Information on Fujitsu | About | Home| MOPAC 93 | 
 MOZYME | This page | Back to
      Home Page. FUJITSU. Inquiries concerning MOPAC 93 and...
      http://iti2.net/jstewart/fujitsu.htm - size 1K - 21 Apr 96 
 
 Project MOPAC
      Project MOPAC Home Page | About | MOPAC 93 | MOZYME | This page | 
 Web-Page:
      HTTP://ITI2.NET/JSTEWART/ Tel: USA+(719) 488-9416 FAX: USA+(719) 
 488-9758....
      http://iti2.net/jstewart/default.htm - size 8K - 20 Apr 96 
 
 Project MOPAC
      Project MOPAC Home Page | About | MOPAC 93 | MOZYME | This page | 
 Web-Page:
      HTTP://ITI2.NET/JSTEWART/ Tel: USA+(719) 488-9416 FAX: USA+(719) 
 488-9758....
      http://iti2.net/jstewart/ - size 8K - 19 Apr 96 
 
 Description of MAKPOL
      Project MOPAC: MAKPOL | About | This page | MOPAC 93 | Back to Home 
 Page | Web-Page:
      HTTP://ITI2.NET/JSTEWART/ Tel: USA+(719) 488-9416 FAX: USA+(719)...
      http://iti2.net/jstewart/makdesc.htm - size 5K - 21 Apr 96 
 
 Omer Casher and Henry Rzepa: Poster
      Omer Casher and Henry Rzepa. Chemical Collaboratories using the 
 Internet. The Explorer EyeChem suite is a
      set of modules suitable for molecular...
      http://www.gene.cinvestav.mx/talks/mgs/poster.html - size 1K - 5 
Apr 
 95 
 
 Results and discussion
      2. RESULTS AND DISCUSSION. The model reaction between 
 alpha-halopenicillins and a methoxide anion
      (serine analogue) was studied at the PM3 or AM1 levels....
      http://www.ch.ic.ac.uk/local/projects/s-smith/project/results.html 
- 
 size 52K - 15 Jun 95 
 
 No Title
      1. F. H. Allen, J. E. Daview, J. J. Galloy, O. Johnson, O. Kennard, 
 C. F. Macrae, E. M. Mitchell, G. F.
      Mitchell, J. M. Smith and D. G. Watson, J. Chem....
      
 http://chem.leeds.ac.uk/papers/html/Perkin2/hyperactive_molecules_fn.html 
 - size 3K - 17 Apr 96 
 
 Casher, Chandramohan, Hargreaves, Leach, Murray-Rust, Sayle, Rzepa, 
 Whitaker
      Hyperactive Molecules and the World-Wide-Web Information System. 
Omer 
 Casher,a. Gudge K.
      Chandramohan,b. Martin J. Hargreaves,b. Christopher J. Leach,a....
      http://chem.leeds.ac.uk/papers/html/Perkin2/tartrazine.html - size 
 
                       Description of MOZYME 
 
   History
   Current Status
   Definition 93
   Capabilities
   Definition
   Examples of Data
   Limitations
   Dynamic Memory
   Bugs fixed

          Top | History | Current Status | Definition | Examples of Data 
| 
 Limitations | Dynamic Memory | Bugs fixed
 
 History of MOZYME
 
 The idea behind MOZYME was conceived on a fishing boat on the way back 
 from the Gothenberg Archepeligo
 during a conference at Aspenas. Prof. Allinger had given some very 
 enjoyable talks on molecular mechanics, and it
 was singularly frustrating to be aware that we could never hope to run 
 such large systems using conventional matrix
 algebra.
 
 Near the end of an afternoon excursion, during which there was a little 
 too much to drink, the idea of using Lewis
 structures as an alternative to matrix algebra was born. Of course, the 
 idea itself was not novel, but perhaps the way
 in which the idea was rendered as method and then as FORTRAN code is 
 novel.
 
 Anyhow, from the start of method development, in May 1993, until now, 
May 
 1996, the project has matured into the
 program MOZYME. The first stage was to do a feasibility study - that 
took 
 about one entire year! After that came
 the extension of the original concept so that it would work for a wide 
 range of systems, and to include the dull but
 essential features such as restarts, data-checking routines, and output 
 routines. Finally, the method was published, and
 many test cases were run, and a distribution tape made, so that 
 researchers could reproduce the calculations
 described in the publications. 

          Top | History | Current Status | Definition | Examples of Data 
| 
 Limitations | Dynamic Memory | Bugs fixed
 
 Current Status of MOZYME
 
 MOZYME is copyrighted software. Fujitsu is the copyright owner. 
 Researchers interested in getting a copy of
 MOZYME should contact Fujitsu. No version of MOZYME will be placed in 
the 
 public domain for the forseeable
 future. 
 
 MOZYME has a limited range of functionalities. Among these are: 
 
    1. 
 
      Electronic Structure Calculations
 
           Restricted Hartree Fock for closed-shell systems. 
    2. 
 
      States
 
            Ground State 
    3. 
 
      Symmetry
 
            None 
    4. 
 
      Geometric Functions
 
            BFGS Geometry Optimizer. 
            Baker's Eigenfollowing Geometry Optimizer 
            Transition State Location for Reactions. 
            Reaction Coordinate Following. 
            Symmetry constraints 
            Ability to specify parameters to be optimized. 
    5. 
 
      Other Capabilities
 
            Solid state (polymers, layers, and solids) 

          Top | History | Current Status | Definition | Examples of Data 
| 
 Limitations | Dynamic Memory | Bugs fixed
 
 Definition of MOZYME
 
 MOZYME is a semiempirical quantum chemical program for the study of 
large 
 systems. The methods in MOZYME
 are similar to those in MOPAC. The fundamental difference is that, 
whereas 
 MOPAC uses matrix algebra for the
 solution of the self-consistent field equations, MOZYME uses localized 
 molecular orbitals. 

          Top | History | Current Status | Definition | Examples of Data 
| 
 Limitations | Dynamic Memory | Bugs fixed
 
 Examples of MOZYME calculations
 
 Examples of systems that have been run successfully using MOZYME are
   Grignard reagent Methyl magnesium bromide can be drawn as a Lewis 
 structure as Me(-) Mg(++) Br(-)
   Benzaldehyde Using localized orbitals, delocalized systems can be 
 modeled.
   Crambin The geometry of a small cross-linked protein is optimized. 
   Poly paraphenylenebenzobisthiazole A highly delocalized 
one-dimensional 
 polymer.
   Boron Nitride A simple two-dimensional layer system.
   DiamondA simple three-dimensional solid
    A Protein from the Brookhaven Protein Data Bank
   Rhizomucor miehei Lipase A large protein.

                                        Examples of Data 
 
 Grignard Reagent
 
 A single-point calculation of Methyl Magnesium Bromide demonstrates that 
 quite complicated Lewis structures can
 readily be handled. 

                                        Examples of Data 
 
 Benzaldehyde
 
 Examination of the 3 dimensional structure of benzaldehyde shows the 
 following Lewis structural elements:
    6 C-H single bonds.
    6 C-C sigma bonds in the aromatic ring.
    1 C-C sigma bond to the carbon of the aldehyde group.
    1 C-O sigma bond.
    3 C=C pi-bonds in the aromatic ring.
    1 C=O pi bond.
    2 lone pairs on the oxygen.
 
 There are thus 18 bonds and 2 lone pairs - these form the occupied set 
of 
 localized molecular orbitals. For every
 bond there is an antibond, therefore there are 18 antibonds. These form 
 the virtual set of LMOs. 
 
 The results of a MOZYME run show that the electronic structure is the 
same 
 as that from MOPAC. In both these
 calculations, the starting points were the same. For this calculation, 
 MOZYME took about 70 seconds to MOPAC's
 13 seconds. Much of the extra time can be accounted for because MOZYME 
 geometry optimizer is less efficient... 

                                        Examples of Data 
 
 Crambin
 
 Crambin is a 46 residue protein found in Abbysinian cabbage seed. From 
the 
 PDB file the 3 dimensional structure
 shows that crambin is highly compact. A 1SCF calculation shows that 7 
 residues are ionized. 
 
 The heat of formation of the optimized geometry is -XXXX kcal/mol. 

                                        Examples of Data 
 
 Poly-paraphenylenebenzobisthiazole

        Like
 MOPAC, MOZYME can model high polymers with large unit cells. Thus PBT, a 
 system with a three ringed
 heterocyclic fragment and one para-phenyl ring per unit cell is best 
 represented in the calculation by three fundamental
 unit cells. The elastic modulus of such a system can be calculated using 
 Hook's law - stretch the unit cell, and monitor
 how the heat of formation changes. 

                                        Examples of Data 
 
 Boron Nitride
 
 Boron nitride illustrates a two-dimensional layer system. For this 
 calculation, 49 fundamental unit cells were used as
 the unit cell. In the calculation, each unit cell is surrounded by 8 = 
 (3**N)-1 other unit cells, where N is the
 dimensionality of the system. After geometry optimization, a 1SCF 
 calculation gives the final electronic structure. 

                                        Examples of Data 
 
 Diamond
 
 Like MOPAC, MOZYME can calculate the electronic structure of 
 three-dimensional systems. A good test case is
 diamond: every atom is in the same environment and any differences in 
the 
 electronic structure of the atoms is an
 indication of errors in the method. Using a cluster of 216 atoms, the 
 results of a 1SCF calculation show that all the
 atoms are, indeed, identical. Making the unit cell bigger, to 512 atoms, 
 did not result in any significant change in the
 electronic structure. 

                                        Examples of Data 
 
 Rhizomucor miehei Lipase
 
 This system has 4,054 atoms. As with crambin, the 3 dimensional 
structure 
 shows that the protein is highly compact.
 A 1SCF calculation shows that 7 residues are ionized.

          Top | History | Current Status | Definition | Examples of Data 
| 
 Limitations | Dynamic Memory | Bugs fixed
 
 Limits of MOZYME
 
   Inadequate testing
 
 Because it is completely new, MOZYME has not been tested in independent 
 laboratories, it has only been tested in
 the laboratory where it was developed. Of course, within a year, this 
 limitation should be corrected. 
 
   No UHF or open shell systems
 
 The only systems that can be run are those for which a Lewis structure 
can 
 be written. Systems allowed include: 
 
 Conventional molecules
 
      benzene, water, proteins, some ions, such as C2H5(-) and NH4(+), 
 polymers, layer systems, and solids. 
 
 Multiple Species
 
      Systems of two or more moieties, such as proteins with many water 
 molecules; proteins composed of two or
      more non-covalently joined chains; ionic systems, such as methyl 
 magnesium bromide (in which the magnesium
      is not bonded to anything, but has a +2 charge); and systems where 
 the various moities are well separated,
      such as CH4 and a distant CH3(+). 
 
 Transition states
 
      Only those transition states for which Lewis structures can be 
drawn 
 are allowed. Thus the TS for 
      CH4 + CH3(+) = CH3(+) + CH4 is allowed, because it can be written 
 with the central hydrogen bonded to
      one carbon, and the charge put on the other carbon. Even though the 
 TS is symmetric, the ONLY requirement
      is that the system can be drawn using Lewis structural elements. 
 
 Hypervalent systems
 
      Only systems that can be written with Lewis structures are allowed. 
 Thus the following hypervalent species can
      be modeled: H2SO4, H3PO4, PO4(3-), Adenosine triphosphate, BF3:NH3, 
 SO2. 
 
 Systems that cannot be modeled include: 
 
 Radicals
 
      Examples: Methyl (CH3.), ethyl (C2H5.), NO2, and the ground state 
of 
 O2. All these systems have open shell
      ground states. 
 
 Electronic Excited States
 
      Closed shell O2, twisted (D2d) ethylene, square cyclobutane. 
 
 Reactions involving open shells
 
      (Suggestions?) 
 
   Other limitations
 
    1. No eigenvectors 
    2. No symmetry recognition 
    3. No solvation models 
    4. No electrostatic potentials 
    5. No vibrational phenomena 

          Top | History | Current Status | Definition | Examples of Data 
| 
 Limitations | Dynamic Memory | Bugs fixed
 
 Memory Requirements of MOZYME
 
 MOZYME uses dynamic memory allocation. A few one-dimensional arrays are 
 'hard wired' in, but all the big arrays
 are assigned at run time. 
 
 As distributed, MOZYME is configured to run systems of up to 10,000 
atoms. 
 If a very small system is run, then the
 size of the running executable is a little less than 2.5 megabytes. The 
 extra memory required for larger systems is
 proportional to the square of the size. This is a result of the 
 electrostatics, which involve every pair of atoms. The
 largest system run during the testing phase was just over 4,000 atoms, 
and 
 that ran in about 400 megabytes. 

          Top | History | Current Status | Definition | Examples of Data 
| 
 Limitations | Dynamic Memory | Bugs fixed
 
 Bugs Corrected
 
 As MOZYME is completely new, no bugs are known at the present time. 
 (1-May-1996) 
 
 c 1996 James J. P. Stewart
 Comments to [email-masked] 
 
 URL:http://iti2.net/jstewart 
 
Thanks a lot to Ed

Rino