This set of tools allows users to automate various tasks related to simulating small molecules using various molecules dynamics techniques. It also contains several python tools for working with small molecules, packing boxes (python wrappers for packmol), and parameterizing small molecules. It also contains tools for creating OpenMM XML forcefield files for small molecules, although we currently focus on the use of AMBER prmtop and inpcrd files due to their widespread use.
Our goal with this project is to have modular components that are both documented and well-tested.
This tool is in BETA testing: use at your own risk!
MolTools is a meant to be used with a number of companion tools: ParmEd, MDTraj, OpenMM, PackMol, OpenEye.
Installation:
python setup.py install
or
conda install -c conda-forge openmoltools
To test your installation, use the following command:
nosetests openmoltools -v --exe
Version 0.8.3 will be the last version of this package to build with Python 2.7. With the OpenEye toolkits no longer being depolyed on Python 2.7 as of 2018.2.1, we have decided to deprecate support for that Python version as well. Version 0.8.3 was tested against the 2017.10.1 version of the OpenEye Toolkits for compatibility.