ParaMol

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

Current Version: 1.1.1

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

The current development version can be installed via conda:

conda install paramol-dev -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 .
• LLS fitting of bonded terms.
• Available symmetrizers: AMBER, GROMACS, CHARMM.
• Optimization algorithms: Scipy Optimizers, Monte Carlo, Gradient Descent, Simulated Annealing.
• QM engines: DFTB+, AMBER, or any QM engine available through ASE.

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 [email protected].

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.