Contents 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

Keywords -- page with Keywords CHARGES ELSTAT_COUPLING_MODEL FORCE_FIELD_FILE LINK_BONDS MASSES MDC_LEVEL MM_CONNECTION_TABLE OPTIMIZE OPTIMIZE: fix_mm_geometry OPTIMIZE: global OPTIMIZE: grid OPTIMIZE: max_gradient OPTIMIZE: max_steps OPTIMIZE: md_search OPTIMIZE: method OPTIMIZE: mm_notconverged OPTIMIZE: print_cycles OUTPUT_LEVEL WARNING_LEVEL

 

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