This set of tools allows users to automate the conversion of ligand force field parameters from Antechamber formats to OpenMM XML format.
This tool is in BETA testing: use at your own risk!
Installation:
python setup.py install
Usage:
mkdir sustiva
cd sustiva
cp ../chemicals/sustiva/sustiva.sdf ./
generate_example_data.py sustiva
This should create a file sustiva.xml, which can be used by openmm to simulate your system.
Under the hood, generate_example_data.py first runs Antechamber then converts
to XML via processAmberForceField.py.
A boilerplate script for simulating your protein-ligand system is available in examples/test_protein_ligand.py
Finally, we recommend that you check agreement (energies and force parameters)
of your XML-based system as compared to creating your system via tleap.
generate_example_data should have already created the necessary inpcrd and prmtop files.
You can evaluate agreement between the XML and prmtop files via the
boilerplate script in examples/test_example.py