General remarks

About this Document

The NEWQMMM subkeyword is available since adf2008.01, which allows large QM/MM calculations. The pdb2adf documentation is available since adf2005.01.

This document describes the QM/MM option within ADF, how to use it, how to set up inputs, what features are available, what its limitations are, and so on. This manual assumes that the reader already has experience with ADF and has some basic knowledge of molecular mechanics (MM) and combined QM/MM theories. A brief overview of the combined QM/MM methods is included.

This document is organized in the following manner. First, concepts and naming conventions that are used throughout the document are introduced. In Chapter 2, setting up a QM/MM simulation with ADF is discussed with a detailed description of all the input options (sections 2.1 and 2.2) and the Force Field files (section 2.3). Section 2.4 contains a ‘walk through’ of how to set up QM/MM jobs.

The combined QM/MM borderleft and the documentation are in continuous development. We appreciate any comments, bug reports and suggestions for its improvement.

Summary of Functionality

Currently, the QM/MM implementation within ADF is based on a modified version [1] of the ‘IMOMM’ scheme of Maseras and Morokuma [2] (called the IMOMM/ADF scheme); alternatively, the recently developed AddRemove scheme [3] is available. The molecular mechanics borderleft has been designed to be as flexible as possible, allowing for many levels of customization. As a result of this flexibility, operation of the program requires the user to have some experience with molecular mechanics methods. At the same time, ADF remains the main driver to control the simulation of the whole QM/MM system, since one of the objectives of the implementation has been to treat the MM subsystem as a perturbation to the QM system.

We summarize the current functionality and limitations of the implementation:

  • Morokuma’s IMOMM [2] QM/MM coupling scheme (IMOMM/ADF).
  • AddRemove [3] coupling scheme.
  • AMBER95 [4] and SYBYL (Tripos) [5] force fields provided.
  • Free form and modifiable force field parameter file.
  • Ability to mix and match force field functions.
  • Geometry optimization, linear transit and transition state optimizations (In these optimizations, the MM region is fully optimized between each SCF cycle or in other words between each QM geometry step).
  • All ADF input ‘styles’ available (Cartesian, Z-matrix, mixed...).
  • Any number of covalent bonds can cross the QM-MM boundary.
  • Global optimization of the MM subsystem available (simulated annealing and grid search algorithms).

Some notable limitations are:

  • Symmetry constraints cannot be applied, unless the MM subsystem is frozen.
  • Geometry constraints involving MM atoms are limited.
  • Not more than one QM atom can be bonded to a single MM atom.
  • Not compatible with some ADF extensions such as NMR, ESR, COSMO, IRC and excited states.
  • The AddRemove model is available only when using Cartesian coordinates.
  • The conjugate gradient optimizer is available only for Cartesian coordinates.

Applicability

This QM/MM implementation evolved from research on organometallic complexes and catalytic systems. Since these systems are generally under 1000 atoms in size, the program had not been optimized to handle large macromolecular systems such as enzymes. In particular, the non-bonded borderleft was not efficient for very large systems. It has been adjusted in the ADF2002.01 release, in order for the borderleft to work efficiently on both small and large systems. Moreover, the calculation of the MM forces has been parallellized to further increase the efficiency and applicability. With the current release, systems with up to several thousand atoms have been tested without problems. Although the input is not designed to handle the topology of macromolecules such as amino acids and peptides, it can be constructed quite easily. For the large systems this amounts however to some 30000 lines; therefore, tools (pdb2adf) have been developed for creating input files automatically for a given PDB-file. This tool is available through a link on the ‘Contributed Software’ part of the SCM web site http://www.scm.com, but is now also part of the official release starting with adf2005.01.

Currently, only the AMBER95 and SYBYL force fields are included. This might also limit the applicability. However, the force field parameters and potentials are fairly customizable and other force fields are easily added.

The utility pdb2adf

Starting from the adf2005.01 version the utility pdb2adf is available in the official release. This utility creates an ADF input file from a PDB file, for a subsequent QM/MM calculation using ADF. This tool has been developed by Marcel Swart. Previously this utility could be found in the contributed software page. Starting from adf2008.01 there is support for the NEWQMMM subkey.