======================
SEAMM QuickMin Plug-in
======================
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A SEAMM plug-in for simple, quick minimization
* Free software: BSD-3-Clause
* Documentation: https://molssi-seamm.github.io/quickmin_step/index.html
* Code: https://github.com/molssi-seamm/quickmin_step
Features
--------
QuickMin provides quick, simple optimization of molecular structures using one of a
number of forcefields. It is intended for small systems, with no more than about 300
atoms. Beyond that size it will be rather slow, but more importantly larger systems
typically have many local minima, often close to each other energetically, so the
concept of the minimum structure is not very useful.
QuickMin uses OpenBabel_ for the minimization. There are currently five forcefields
available:
#. GAFF_ -- the general AMBER force field
#. MMFF94_ -- the Merck molecular force field
#. MMFF94s_ -- the Merck molecular force field for energy minimization
#. Ghemical_
#. UFF_ -- Universal force field
The first four have parameters for organic and biomolecular systems, while UFF attempts
to cover the entire periodic table with reasonable accuracy. The more specialized
forcefields tend to be more accurate, roughly in the order listed (though the two MMFF94
are essentially similar). By default QuickMin will try each of the forcefields in the
order given until it finds one that can handle the given molecule. You can specify the
forcefield to use; however, if it does not have parameters for your molecule, QuickMin
will throw an error.
.. _OpenBabel: http://openbabel.org/wiki/Main_Page
.. _GAFF: https://ambermd.org/antechamber/gaff.html
.. _MMFF94: https://onlinelibrary.wiley.com/doi/10.1002/%28SICI%291096-987X%28199604%2917%3A5/6%3C490%3A%3AAID-JCC1%3E3.0.CO%3B2-P
.. _MMFF94s: https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291096-987X%28199905%2920%3A7%3C720%3A%3AAID-JCC7%3E3.0.CO%3B2-X
.. _Ghemical: http://bioinformatics.org/ghemical/ghemical/index.html
.. _UFF: https://pubs.acs.org/doi/10.1021/ja00051a040
Acknowledgements
----------------
This package was created with the `molssi-seamm/cookiecutter-seamm-plugin`_ tool, which
is based on the excellent Cookiecutter_.
.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`molssi-seamm/cookiecutter-seamm-plugin`: https://github.com/molssi-seamm/cookiecutter-seamm-plugin
Developed by the Molecular Sciences Software Institute (MolSSI_), which receives funding
from the `National Science Foundation`_ under award CHE-2136142.
.. _MolSSI: https://molssi.org
.. _`National Science Foundation`: https://www.nsf.gov
=======
History
=======
2023.11.15 -- Bugfix: structure handling
Error putting the coordinates into a newly created configuration.
2023.10.30 -- Enhanced structure handling.
Switched to standard handling of structures, which adds ability to name with the
IUPAC name, InCHI, and InChIKey in addition to previous methods.
2023.1.14 -- Changed documentation to new style and theme.
Switched the documentation to the MolSSI theme and diátaxis layout, though more work
is needed.
2022.11.7 -- Internal Release
Switching from LGTM code analysis to GitHub Actions using CodeQL, since LGTM is
shutting down!
2022.10.23 -- Properties added
Added a single property, 'total energy#QuickMin#<forcefield>', to store the final
energy in the database. Also added 'total energy' as a result for tables or
variables.
2022.10.22 -- Documentation!
Got the documentation into reasonable shape.
2022.10.20 -- Initial Release!
Provides quick minimization for smaller molecules, using OpenBabel. Probably
reasonable for some few hundred atoms. Supports the following forcefields:
1. GAFF
2. MMFF94 & MMFF94s (which is optimized for minimization)
3. Ghemical
4. UFF
The default is the "best available" forcefield, which tries them in the order given
above until it finds one that can handle the molecule.
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By default QuickMin will try each of the forcefields in the\norder given until it finds one that can handle the given molecule. You can specify the\nforcefield to use; however, if it does not have parameters for your molecule, QuickMin\nwill throw an error.\n\n.. _OpenBabel: http://openbabel.org/wiki/Main_Page\n.. _GAFF: https://ambermd.org/antechamber/gaff.html\n.. _MMFF94: https://onlinelibrary.wiley.com/doi/10.1002/%28SICI%291096-987X%28199604%2917%3A5/6%3C490%3A%3AAID-JCC1%3E3.0.CO%3B2-P\n.. _MMFF94s: https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291096-987X%28199905%2920%3A7%3C720%3A%3AAID-JCC7%3E3.0.CO%3B2-X\n.. _Ghemical: http://bioinformatics.org/ghemical/ghemical/index.html\n.. _UFF: https://pubs.acs.org/doi/10.1021/ja00051a040\n\nAcknowledgements\n----------------\n\nThis package was created with the `molssi-seamm/cookiecutter-seamm-plugin`_ tool, which\nis based on the excellent Cookiecutter_.\n\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _`molssi-seamm/cookiecutter-seamm-plugin`: https://github.com/molssi-seamm/cookiecutter-seamm-plugin\n\nDeveloped by the Molecular Sciences Software Institute (MolSSI_), which receives funding\nfrom the `National Science Foundation`_ under award CHE-2136142.\n\n.. _MolSSI: https://molssi.org\n.. _`National Science Foundation`: https://www.nsf.gov\n\n\n=======\nHistory\n=======\n2023.11.15 -- Bugfix: structure handling\n Error putting the coordinates into a newly created configuration.\n \n2023.10.30 -- Enhanced structure handling.\n Switched to standard handling of structures, which adds ability to name with the\n IUPAC name, InCHI, and InChIKey in addition to previous methods.\n\n2023.1.14 -- Changed documentation to new style and theme.\n Switched the documentation to the MolSSI theme and di\u00e1taxis layout, though more work\n is needed.\n \n2022.11.7 -- Internal Release\n Switching from LGTM code analysis to GitHub Actions using CodeQL, since LGTM is\n shutting down!\n \n2022.10.23 -- Properties added\n Added a single property, 'total energy#QuickMin#<forcefield>', to store the final\n energy in the database. 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