An extensible interface for QM/MM molecular dynamics simulations with AMBER

Abstract

We present an extensible interface between the AMBER molecular dynamics (MD) software package and electronic structure software packages for quantum mechanical (QM) and mixed QM and classical molecular mechanical (MM) MD simulations within both mechanical and electronic embedding schemes. With this interface, ab initio wave function theory and density functional theory methods, as available in the supported electronic structure software packages, become available for QM/MM MD simulations with AMBER. The interface has been written in a modular fashion that allows straight forward extensions to support additional QM software packages and can easily be ported to other MD software. Data exchange between the MD and QM software is implemented by means of files and system calls or the message passing interface standard. Based on extensive tests, default settings for the supported QM packages are provided such that energy is conserved for typical QM/MM MD simulations in the microcanonical ensemble. Results for the free energy of binding of calcium ions to aspartate in aqueous solution comparing semiempirical and density functional Hamiltonians are shown to demonstrate features of this interface.

Small Details Matter: The 2′-Hydroxyl as a Conformational Switch in RNA

“…They include the following: (i) standard simulations in hairpin and kissing loop RNA motives ; (ii) potentials of mean force (PMF) of the  rotation at the dinucleotide (rCpC) level using umbrella sampling (US) with an 18° interval grid of the κ torsional space (500 ps equilibration and 2.5 ns of averaging per window); and (iii) Hamiltonian-replica exchange molecular dynamics (H-REMD) to evaluate the conformational landscape of two small RNA tetranucleotides (rGACC and rCCCC) for which experimental structural data in solution are available. 19,20 All calculations were performed using the parm99 force field 21,22 supplemented with the bsc0 23 and chiOL3 24,25 modifications for RNA; some control simulations were performed with a local experimental RNA version of the parmbsc1 forcefield. 26 Electroneutrality was achieved by adding K + and extra K + Cl -to generate a 150 mM concentration (taking Dang's parameters [27][28][29] to represent ions).…”

Probing the Catalytic Mechanism Involved in the Isocitrate Lyase Superfamily: Hybrid Quantum Mechanical/Molecular Mechanical Calculations on 2,3-Dimethylmalate Lyase

“…[20][21][22] In particular, the combined quantum mechanics and molecular mechanics (QM/MM) approaches have been using to gain insight of the catalytic mechanisms where the chemical reactions take place. [22][23][24][25][26] In this method the active site region is modelled QM and the surrounding protein and solvent are treated using less computationally demanding MM. The method has been used in the past to study drug metabolism at Cytochrome P450s, 27 investigate suicidal inhibitors 28,29 and indeed re-evaluate mechanisms of well-known proteins.…”

iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings

“…These methods are currently supported only for the AMBER software package, which enables QM/MM MD, 17 semiempirical Born–Oppenheimer MD (SEBOMD 18 ), and multidimensional replica-exchange MD. 15 A current list of the file formats and computational methods supported by the parsers is available on the Wiki at .…”