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

• Published in: Journal of computational chemistry 2023-02, Vol.44 (4), p.516-533
• Main Authors: Cárdenas, Gustavo, Lucia‐Tamudo, Jesús, Mateo‐delaFuente, Henar, Palmisano, Vito F., Anguita‐Ortiz, Nuria, Ruano, Lorena, Pérez‐Barcia, Álvaro, Díaz‐Tendero, Sergio, Mandado, Marcos, Nogueira, Juan J.
• Format: Article
• Language: English
• Subjects: Absorption spectra; Acetonitrile; Active Space; Azo Compounds; Electrostatic Embedding; Emission spectra; Energy Decomposition Analysis; Ion channels; Mathematical analysis; Molecular Dynamics; Molecular Dynamics Simulation; Molecular structure; Open‐source QM/MM software; Organic chemistry; Photochemistry; Programming languages; Quantum mechanics; Quantum Theory; Reduction Potentials; Software; Toolkits; Topology; Tyrosine
• ISSN: 0192-8651; 1096-987X; 1096-987X
• DOI: 10.1002/jcc.27018

We present a toolkit that allows for the preparation of QM/MM input files from a conformational ensemble of molecular geometries. The package is currently compatible with trajectory and topology files in Amber, CHARMM, GROMACS and NAMD formats, and has the possibility to generate QM/MM input files for Gaussian (09 and 16), Orca (≥4.0), NWChem and (Open)Molcas. The toolkit can be used in command line, so that no programming experience is required, although it presents some features that can also be employed as a python application programming interface. We apply the toolkit in four situations in which different electronic‐structure properties of organic molecules in the presence of a solvent or a complex biological environment are computed: the reduction potential of the nucleobases in acetonitrile, an energy decomposition analysis of tyrosine interacting with water, the absorption spectrum of an azobenzene derivative integrated into a voltage‐gated ion channel, and the absorption and emission spectra of the luciferine/luciferase complex. These examples show that the toolkit can be employed in a manifold of situations for both the electronic ground state and electronically excited states. It also allows for the automatic correction of the active space in the case of CASSCF calculations on an ensemble of geometries, as it is shown for the azobenzene derivative photoswitch case. Herein, we present MoBioTools, a toolkit to set up in an automatic manner QM/MM calculations on ensembles of geometries to be performed by several commonly used software packages for quantum chemistry calculations. The toolkit is characterized by the variety of situations it can be applied on, as well as the simplicity it can be employed with, by an execution in command line. We apply the toolkit in four different situations: the reduction potential of the nucleobases in acetonitrile, an energy decomposition analysis of tyrosine interacting with water, the absorption spectrum of an azobenzene derivative integrated into a voltage‐gated ion channel, and the absorption and emission spectra of the luciferine/luciferase complex. The toolkit also features an automatic corrector of the active space for CASSCF calculations on ensembles of geometries.