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

Abstract

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.

The Protein Environment Restricts the Intramolecular Charge Transfer Character of the Luciferine/Luciferase Complex

“…From each of the 100 ns simulations in the S 0 and S 1 electronic states, 200 time-equidistant snapshots were extracted from the last 75 ns in order to prepare the Gaussian09 QM/MM input files for the calculation of the absorption and emission spectra. The MoBioTools software 89 was used to automatized the preparation of the QM/MM input files, which considered 10 excited states (for the absorption spectrum) at the TD-B3LYP/6-311G(2d,p) level of theory. In the case of the emission spectrum, only the lowestenergy electronic transition was considered since the bioluminescence occurs from the S 1 state.…”

“…The preparation of the Gaussian09 70 input files was again performed by means of the MoBioTools software. 89…”

The protein environment restricts the intramolecular charge transfer character of the luciferine/luciferase complex

“…From each of the 100 ns simulations in the S 0 and S 1 electronic states, 200 time-equidistant snapshots were extracted from the last 75 ns in order to prepare the Gaussian09 QM/MM input files for the calculation of the absorption and emission spectra. The MoBioTools software 92 was used to automatize the preparation of the QM/MM input files, which considered 10 excited states (for the absorption spectrum) at the TD-B3LYP/ 6-311G(2d,p) level of theory. In the case of the emission spectrum, only the lowest-energy electronic transition was considered since the bioluminescence occurs from the S 1 state.…”

“…The preparation of the Gaussian09 68 input files was again performed by means of the MoBioTools software. 92…”

Automatic Rhodopsin Modeling with Multiple Protonation Microstates

“…87 The rPSB geometry was extracted from one of the ARM CASSCF-optimized geometries for the toy model, and the OpenMolcas inputs were generated using the MoBioTools toolkit. 88…”