MoBioTools: A toolkit to setup quantum mechanics/molecular mechanics calculations

Area of Science:

• Computational Chemistry
• Molecular Modeling
• Biophysics

Background:

• Preparing input files for QM/MM calculations from molecular dynamics trajectories is often complex and time-consuming.
• Existing tools may lack compatibility with diverse simulation packages or quantum chemistry codes.

Purpose of the Study:

• To introduce a user-friendly toolkit for generating QM/MM input files from conformational ensembles.
• To facilitate the study of electronic structure properties of molecules in various environments.

Main Methods:

• The toolkit processes trajectory and topology files from Amber, CHARMM, GROMACS, and NAMD.
• It generates input files for quantum chemistry software including Gaussian, Orca, NWChem, and (Open)Molcas.
• The toolkit offers both command-line and Python API interfaces.

Main Results:

• The toolkit was successfully applied to diverse systems, including nucleobases in solution, amino acids in water, and photoswitch molecules in biological channels.
• It enabled computation of ground and excited electronic states, such as reduction potentials and absorption/emission spectra.
• Automatic active space correction for CASSCF calculations on ensembles was demonstrated.

Conclusions:

• The presented toolkit significantly streamlines the QM/MM workflow for computational studies.
• Its versatility and ease of use make it valuable for investigating complex molecular systems and properties.