QUBEKit - Quantum Mechanical Bespoke force field toolkit examples
Newcastle University UK - Cole Group
This repository contains examples on how to use QUBEKit from both the command line as an python library.
Demonstration day
This folder contains all of the files used during the Newcastle PGR conference live density prediction demo. We also have a notebook on how to recreate the results.
Protein examples
QUBEKit-pro can also handel protein parametrisation and this folder shows how QUBEKit can be used to generate a ONETEP input and then parametrise a protein ready for an OpenMM simulation from the command line.
ARChive fitting
This folder contains two scripts VEHICLe_QUBEKit.py and Torsion_fitting.py. They should how QUBEKit can be used to determine bond and angle parameters for a molecule from QCArchive using the modified seminario method and how we can use QUBEKit to optimise a dihedral using torsion drive data from the Archive respectively. A note book is also included for torsion_fitting which also covers visualising the results.