| What is MoCalc | Copyright |
| Team | How to cite |
| Features | User's guide |
| Snapshots | Download |
What is MoCalc?
MoCalc: Molecular Calculation Interface is a graphical user interface for the molecular modeling programs Gamess1, Mopac2, Tinker3, Babel4 and Rasmol5. MoCalc helps the user in the preparation of input files, the submission of calculations, the analysis of the results and the visualization of the involved chemical structures. Some properties can also be calculated by MoCalc.
The construction of MoCalc system followed the conventional pattern adopted for programs designed for Microsoft Windows environment. The users familiar with this operating system won't have difficulties in most of the tasks MoCalc is capable to execute.
The MoCalc development team has made a great effort to create a useful scientific tool. In the coming years, we will try to improve the MoCalc operation capabilities so that it can become more powerful and easier to use. We hope MoCalc can satisfy your expectancy.
References:
- Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S.; Windus, T. L.; Dupuis, M.; Montgomery, J. A., Jr.; General Atomic and Molecular Electronic Structure System. Journal of Computational Chemistry, 14, 1347-1363, 1993.
- Stewart, J. J. P.; MOPAC: A Semiempirical Molecular Orbital Program. Journal of Computer-Aided Molecular Design, 4, 1-105, 1990.
- TINKER Software Tools for Molecular Design, 3.7; Jay Ponder Lab, Dept. of Biochemistry & Molecular Biophysics, Washington University School of Medicine: St. Louis, 1999.
- Walters, P.; Stahl, M.; Babel, Versão V.1.6, 1994.
- RasMol: Molecular Visualisation Program, Versão 2.7; Glaxo Wellcome Research and Development, Stevenage, Hertfordshire, 1995.
Features
Release 2.2:
- Create and handle Gamess, Mopac, and Tinker input files;
- Fast conversion of Gamess, Mopac, and Tinker input and output files, through the Babel program. The conversion may involve several files in just one procedure;
- Fast conversion of external files of the types Gamess output, Mopac input, Mopac output, Tinker input, Hyperchem, Protein Data Bank, Sybyl, and Spartan;
- Import multiple external files of types Gamess output, Mopac input, Mopac output, Tinker input, Hyperchem, Protein Data Bank, Sybyl, and Spartan to MoCalc system, converting them from their original format into Gamess input, Mopac input, or Tinker input document;
- Edit and validate the keywords $CONTRL, $SYSTEM, $BASIS,$DRC, $FORCE, $MOROKM, $MP2, $PCM, $SCF and $STATPT that control the Gamess calculation procedure;
- Edit and validate all keywords that control the Mopac calculation procedure;
- Display the input (Mopac and Tinker) and output (Gamess, Mopac, and Tinker) molecular geometries through the RasMol program;
- Run single or multiple (batch) calculations, either interactively or in background, and automatically open the output files as soon as the calculation finishes;
- Energy minimization and global minimum energy search can be proceed through molecular mechanics (MM3) methodology; Calculation of molecular surface area and volume, and vibrational analysis;
- Extract results from the output files, such as energy, charges, dipole, interatomic distances, population analysis, wave function, bond orders, and valence analysis, and display them in spreadsheets;
- Calculate reactivity indices derived from the frontier orbital theory and the root mean square (RMS) deviation of input and output geometries;
- All results generated by MoCalc can be immediately transferred to text editors and spreadsheets;
- The calculation results can be exported to HTML files;
- When more than one Gamess/Mopac output files are opened, MoCalc can run a comparative analysis of the results in those files by showing the values of many properties in a spreadsheet. MoCalc also generate a graphical comparison of these properties;
- Graphical interface with menu and pop up menu system, toolbar, status bar, pathname bar, and file tree display;
- The pop up menu system allow the user to run calculation and handle Gamess, Mopac, and Tinker documents;
- MoCalc is available only in English;
- Complete English help file in PDF format;
- Gamess, Mopac, Tinker, Rasmol, and Babel manuals available.
Snapshots
Some snapshots of software MoCalc follow:
- MDI (Multiple Document Interface) environment of MoCalc:
- Multiple document opening form:
- Gamess keyword editor:
- Form used to import external molecular geometry to Gamess e Mopac input documents:
- Molecular geometry visualization through RasMol program:
- Properties extracted from Gamess and Mopac output files can be showed in spreadsheets:
- Form used to run single and multiple calculations:
- Numerical comparison of some properties extracted from many Gamess and Mopac output files are showed in a spreadsheet:
- Graphical comparison of some properties extracted from many Gamess and Mopac output files are showed in form:
- MoCalc manual:
Team
Project manager:
Anderson Coser Gaudio
Undergraduate students:
Daniela Bertolini Depizzol
Marcia Helena Moreira Paiva
Thiago Oliveira dos Santos
Copyright
Except where otherwise noted, all of the documentation and software included in the MoCalc Setup package is copyrighted by Anderson Coser Gaudio.
Copyright (c) 2004-2006 Anderson Coser Gaudio. All rights reserved.
MoCalc 2.1 is a FREEware (NOT a public domain software) which means that you can use this software for any purpose, including commercial applications, as long as you need, make as many copies as you want and freely distribute it, provided that all the files are included and are unmodified and that no files have been added to the package. Please distribute it by copying the original self-extracting setup file MoCalcSetup.exe. It is FORBIDDEN to ask money or anything else for the distribution. Only the copyright owner may beg for voluntary cash donation that will always be completely independent from the program distribution. Any money sent to the copyright owner will be fully employed in the development of future versions of MoCalc and other free-distributable applications.
However, you may NOT attempt to reverse compile, modify, translate or disassemble any parts of the software. NOTE: if you have modified one or more components of MoCalc, you may NOT distribute it as part of our program any longer. If you want to put this component on a freeware CD-ROM or in other compilation, please contact us before doing so, to be sure that you are not including old, incompatible, or incomplete stuff in the compilation. We would also appreciate it if we could get a free copy of the CD-ROM.
Also, we need to mention that Gamess, Mopac, Tinker, RasMol, and Babel programs, and the respective user manuals, are NOT our property. Gamess belongs to the Mark Gordon's Quantum Theory Research Group, Ames Laboratory, Iowa State University, which exclusively distributes it. Mopac belongs to the United States of America government. Tinker is property of Jay William Ponder, Biochemistry & Molecular Biophysics, Washington University School of Medicine, USA, Rasmol belongs to Roger Sayle, Glaxo Wellcome Research and Development, Stevenage, Hertfordshire, UK. Babel belongs to Pat Walters and Matt Stahl, Dolata Research Group, Department of Chemistry, University of Arizona, Tucson, AZ 8572.
This software is provided "as is". In no event shall we, the authors, be liable for any consequential, special, incidental or indirect damages of any kind arising out of the delivery, performance or use of this software. This software has been written with great care but I do not warrant that the software is error free.
Dr. Anderson Coser Gaudio
Physics Department
Federal University of EspÃrito Santo
Campus Universitário "Alaor de Queiroz Araújo"
Av. Fernando Ferrari, 514 - Goiabeiras
29075-910 Vitória, ES
Brazil
How to Cite
After using MoCalc for any purpose, please cite it as following:
Depizzol, D.B.; Paiva, M.H.M.; Dos Santos, T.O.; Gaudio, A. C.; MoCalc: A New Graphical User Interface for Molecular Calculations. J. Comput. Chem, 26(2), 142-144, 2005.
User's Guide
Click here to open the PDF version of MoCalc user's guide.
Download
Click here to freely download MoCalc.