Kick3 (position, orientation, conformation) is a stochastic structure generator. Fully rewritten from the original perl to employ the Python ASE (https://wiki.fysik.dtu.dk/ase/faq.html), it can generate structures ranging from 0-D (clusters), through to 3-D periodic boxes. Fragments input to the program may likewise range from atoms, to molecules – which may be flexible or rigid) and periodic assemblies (e.g. frameworks).
Code is available for free (as in beer) download via github: http://maddicoat.github.io/Kick3/
J. Comput Chem, 30, 2013, 2591-2600
Front cover: http://onlinelibrary.wiley.com/doi/10.1002/jcc.v34.30/issuetoc
AuToGraFS is the Automatic Topological Structure Generator for Framework Structures. It is written in python and uses a customised version of the Python ASE. Structures are optimised using UFF4MOF. The basic (command line only) version of AuToGraFS is available from github: (https://github.com/maddicoat/AuToGraFS). It is also implemented with full GUI support by SCM (https://www.scm.com/doc/Scripting/AuToGraFS/AuToGraFS.html)
AuToGraFS is continually being extended (albeit slowly), so send me an email if something you need isn’t there.
J. Phys Chem A, 118, 2014, 9607-9614
The Universal Force Field has been around since 1992 and is a fantastic way of getting a quick answer for any chemical structure, no matter what atoms it contains. The problem when applying it to MOF structures is that for some metals (e.g. Copper and Zinc), UFF assumed the metal was tetrahedrally coordinated, not octahedral. In UFF4MOF we found all the cases where UFF was missing a parameter and derived new ones specifically for MOF structures.
J. Chem. Theory Comput., 2014, 10, 880–891
J. Chem. Theory Comput., 2016, 12, 5215–5225
And including hydrogen bonds:
J Chem Phys, 147, 2017, 161705