DivCon Command Line (qmechanic)

qmechanic is a Command Line Interface client built on top of the QuantumBio Toolkit. It provides a text-based interface to execute calculations on computational clusters, within scripts, or in similar enviroments.

The command line client is highly performant with pervasive multithreading and methodological optimizations. The tool is extremely user friendly and supports a wide range of applications. With a system built on divide and conquer, linear scaling, quantum mechchanics, the client is able to treant a whole protein:ligand complex at a semiempirical level of theory. Further, the tool includes   linear scalingsupports full QM, ONIOM (QM/MM) with multiple QM regions, automated AMBER atom typing, and formal charge determination.

Some key features include:

  • Fully automatic atom type perception
  • Macromolecular characterization (including heat of formation, electronic energies, atomic charges, and so on)
  • Structure optimization and gradient generation
  • Interaction energy decomposition to explore the interactions between a protein and its ligand.
  • Nuclear Magnetic Resonance for chemical shift perterbation (CSP) prediction
  • Support for the AM1, PM3, and PM6 quantum mechanics Hamiltonians
  • Molecular mechanics force field support including AMBERFF94, AMBERFF99, AMBERFF10, AMBERFF12, AMBERFF14, and the Generalized AMBER Force Field (GAFF). 

 

The Divide and Conquer Method

 

 

The method implemented in the DivCon Discovery Suite automatically divides the structure into its component parts based on the residue configuration of the macromolecule. Each residue acts as a core and the buffer region is extended to the surrounding residues in order capture the interactions between the core and its environment.

This configuration is represented in the figure above. The buffer radius, the arrow in the figure, is set by default to 5.0 Å. Any residue that has an atom which falls within that radius is included within the buffer. This "residue extended" buffer region is made up of the blue residues. By dividing the system into smaller parts, the matrix diagonalization (e.g. the most expensive part of the calculation) is performed on smaller matrices.

When this method is coupled with a molecular mechanics (MM) implementation of the AMBER force field, you can treat even larger structures with QM/MM!

 

Toolkit Applications