James J. P. Stewart and Anna C. Stewart
Stewart Computational Chemistry, 15210 Paddington Circle, Colorado Springs, CO 80921, USA
Email: MrMOPAC@att.net
| Tables | ||
| 1 | See Entry 5 | |
| 2, 3 | See Entry 13 | |
| 5 | See Entry 2 (To reproduce Clashscores, use the PDB files in this page) | |
| 6 | See Entry 3 (To reproduce RMS difference, use the ARC files from Entry 2) | |
| 7 | See Entry 2 (To see volumes, see ARC files from Entry 2) | |
| 8 | See Entry 2 and Entry 4 | |
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Entry
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Contents |
Description |
| 1 | Accuracy of PM6-ORG PM6-D3H4X and PM7 | Results and statistics for heats of formation, non-covalent interactions, dipole moments, geometries, and ionization potentials |
| 2 | Results for proteins reported in the paper | PDB, PM6-ORG, PM6-D3H4, and PM7 information on the 21 proteins. This includes Jmol GUI, Optimized geometries, PDB files, and information in various tables |
| 3 | Compare PM6-ORG and PDB protein geometries | Compare complete and backbone only geometries for X-ray PDB and optimized PM6-ORG structures |
| 4 | Excel spreadsheet of results reported in the paper (25 Kb) | Similar to Entry 2, but in Microsoft Excel format |
| 5 | Files for parameterization operations (33 Mb) | Source code for MOPAC and PARAM, Training set of reference data, parameterization data sets, and output files, and survey files |
| 6 | PARAM Manual | Description of PARAM, keywords, and how to use it. |
| 7 | MOPAC and PARAM source-code (8.2Mb) | Source code and compiling instructions for MOPAC and PARAM |
| 8 | MOPAC and PARAM executables for Windows (13.6 Mb) | These three versions of MOPAC and PARAM have default names. If necessary, change the names to suit local conditions. Note that the executables are specific for the versions of MOPAC and PARAM used in parameterization, this ensures that the material presented can be reproduced.. |
| 9 | MOPAC and PARAM executables for MacOS (12.8 Mb) | |
| 10 | MOPAC and PARAM executables for Linux (12.8 Mb) | |
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Programs for working with reference data
files |
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| 11 | Source code for program "Files" (20 Kb) | Works in a folder that contains reference data. Generates a file, "files.out", that will be used by "Select" to make a sub-set for use in parameterization, surveys, etc. |
| 12 | Source code for program "Select" (7 Kb) | Works in a folder that contains reference data. Selects all reference data files that contain the set of elements defined at run-time |
| 13 | Utilities for generating tables of results for individual survey data sets and statistics of errors for those sets. | |
| 14 | PM6-D3H4 water hydrogen bonds | Examples of a water molecule forming two hydrogen bonds with the same oxygen atom acceptor. To see these structures, use information in Entry 2 |