ParaMol

ParaMol is a Python library that aims to ease the process of force field parametrization of molecules.

Current Version: 1.1.4

Quick Installation

The easiest way to install ParaMol it.

The last stable version can be installed via conda:

conda install paramol -c jmorado -c ambermd -c conda-forge -c omnia -c rdkit -c anaconda

Available Tasks

• Parametrization.
• LLS fitting.
• Adaptive parametrization.
• RESP charge fitting.
• ab initio properties calculation.
• Objective function plot.
• Torsional scans.
• Automatic parametrization of soft torsions.

Current features

• Parallel and serial computation of the objective .</li>
• LLS fitting of bonded terms. </li>
• Available symmetrizers: AMBER, GROMACS, CHARMM.
• Optimization algorithms: Scipy Optimizers, Monte Carlo, Gradient Descent, Simulated Annealing.</li>
• QM engines: DFTB+, AMBER, or any QM engine available through ASE.</li>

Tests

ParaMol uses the pytest framework to test the code. pytest can be install through pip:

pip install -U pytest

Once pytest is installed, the tests can be run by simply typing:

python -m pytest

in ParaMol's root directory.

Contact

ParaMol is developed and maintained by João Morado at the University of Southampton.

If you have any question or issue to report please contact j.morado@soton.ac.uk.

References

Morado, J.; Mortenson, P. N.; Verdonk, M. L.; Ward, R. A.; Essex, J. W.; Skylaris, C.-K. ParaMol: A Package for Automatic Parameterization of Molecular Mechanics Force Fields. J. Chem. Inf. Model. 2021, acs.jcim.0c01444. https://doi.org/10.1021/acs.jcim.0c01444.

Notes

This library is no longer under active development.