Table of Contents

ADF QM/MM
Table of Contents
1 Introduction
1.1 General remarks
About this Document
Summary of Functionality
Applicability
The utility pdb2adf
1.2 Concepts and Terminology
LINK bonds
The ADF QM/MM Hybrid Potential
Nomenclature and Terminology
Full QM/MM system vs. QM model system
Link bonds and capping atoms
QM, MM and LI atom types
Atom types
QM/MM type or QM/MM atom type (MM, QM or LI)
Force Field atom type
ADF atoms or ADF fragments
Partitioning into QM and MM regions
1.3 Implementation
ADF QM/MM
Limitations, Bugs and Deficiencies
2 ADF QM/MM
2.1 Input: The Essentials
Overview
Example Input
Defining the Coordinates
QMMM key block
Restarts
Geometry Constraints and Fixing Coordinates of MM atoms
Miscellaneous Notes
2.2 QMMM keyblock options
Introduction
Example Input
Description of Options
2.3 The Force Field File
General Notes
Format
Force Field Atom types
Wild Cards
Dummy Atoms
Miscellaneous Notes
Section by Section Description
2.4 Setting up a QM/MM Simulation: a 'Walk Thru'
Example A: Cytocine
Step 1. Partitioning the System and the Model QM system
Step 2. Labeling of Atoms (QM, MM or LI)
Step 3. Renumbering of Atoms
Step 4. ADF QM/MM input: Atomic coordinates
Step 5. Connection Table and MM force field types
Step 6. LINK_BONDS
Step 7. Assignment of Atomic Charges
Step 8. Remainder of the QMMM key block
Step 9. Putting it all together: The whole ADF QM/MM input
Example B: Pd⁺-Ethene pi-complexation Linear Transit
Step 1. Partitioning the System and the Model QM system.
Step 2. Labeling of Atoms
Step 3. Renumbering of Atoms
Step 4. Z-matrix and constraints
Step 5. Connection Table, MM force field atom-types and Force Field Modification
Step 6. LINK_BONDS
Step 7. CHARGES
Step 9. Putting it all together: The whole ADF QM/MM input.
3 pdb2adf: transform PDB file to QM/MM input file
3.1 Overview
General description
Things to notice
Official PDB format
Contents of fragment file
Contents of solvent box files
3.2 Usage of pdb2adf
Short description
An example on protein structure
Usage of pdb2adf
Contents of the 1DYZ.pdb2adf file generated by pdb2adf
An example on solvent shell run
Contents of the hoh.pdb file
Usage of pdb2adf
Contents of the hoh.pdb2adf file generated by pdb2adf
References
Appendix A. List of Publications Using ADF QM/MM
Keywords

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