The CHARMM–TURBOMOLE interface for efficient and accurate QM/MM molecular dynamics, free energies, and excited state properties

Abstract

The quantum mechanical (QM)/molecular mechanical (MM) interface between Chemistry at HARvard Molecular Mechanics (CHARMM) and TURBOMOLE is described. CHARMM provides an extensive set of simulation algorithms, like molecular dynamics (MD) and free energy perturbation, and support for mature nonpolarizable and Drude polarizable force fields. TURBOMOLE provides fast QM calculations using density functional theory or wave function methods and excited state properties. CHARMM-TURBOMOLE is well-suited for extended QM/MM MD simulations using first principles methods with large (triple-ζ) basis sets. We demonstrate these capabilities with a QM/MM simulation of Mg(2+) (aq), where the MM outer sphere water molecules are represented using the SWM4-NDP Drude polarizable force field and the ion and inner coordination sphere are represented using QM PBE, PBE0, and MP2 methods. The relative solvation free energies of Mg(2+) and Zn(2+) were calculated using thermodynamic integration. We also demonstrate the features for excited state properties. We calculate the time-averaged solution absorption spectrum of indole, the emission spectrum of the indole 1La excited state, and the electronic circular dichroism spectrum of an oxacepham.

Tuning the Protein‐Induced Absorption Shifts of Retinal in Engineered Rhodopsin Mimics

“…The classical relaxation of the systems was carried out using NAMD2 . The quantum chemical calculations were performed using TURBOMOLE versions 6.5 and 6.6, and the QM/MM calculations were performed with CHARMM/TURBOMOLE . Visual Molecular Dynamics (VMD) was used for analysis of the results, and electrostatic potentials at T= 298 K were calculated by solving the linearized Poisson–Boltzmann Equation using APBS …”

Symmetry-related proton transfer pathways in respiratory complex I

“…The MM system comprised the Nuo12/13/14 subunits and surrounding lipids and water molecules, with a total system size of approximately 75,000 atoms. The QM/MM MD simulations were simulated for 5 ps each, using a 1-fs integration time step, and a temperature of T = 310 K. The simulations were performed using the CHARMM/TURBOMOLE interface (71)(72)(73). Proton transfer from Lys-235 13 to Glu-377 13 .…”

Prediction of Molecular Interaction between Platelet Glycoprotein Ibα and von Willebrand Factor using Molecular Dynamics Simulations

“…We have applied the established calculation software named NAMD package 52) with the CHARMM 22 [53][54][55][56] for simulating molecular interaction between A1 domain of VWF and N-terminus domain of GPIb . By Monte-Carlo simulation, we have previously shown that the localization GPIb is a key determinant factor for platelet binding with large size of VWF molecule 57) .…”