🇭🇺 Magyar

Molecular Modeling and Artificial Intelligence SU project documentation

This documentation is intended for use with the installed molecular modeling and simulation software packages within the framework of the SU project. It aims to provide users with a comprehensive, yet practice-oriented guide.

Table of contents

• Introduction
  • Code Examples
  • Command-Line (Bash) Instructions
  • Input Files
  • Output Files
  • Notes and Warnings
  • Summary of Conventions
• AlphaFold 3
  • Introduction
  • Reference Structure
  • Workflow Overview
  • Sequence Preparation
  • Downloading the FASTA Sequence from the PDB Database
  • Input JSON File Creation
  • Directory Structure and Execution
  • Output Files
  • Visualizing the Predicted Structure in ChimeraX
• AMBER
  • Obtaining and Preparing the PDB File
  • Generating Topology and Coordinate Files with LEaP
  • Energy Minimization
  • System Heating
  • Equilibration
  • Production Stage
  • Analysis: Trajectory RMSD and Hydrogen Bond Count Using cpptraj
• AutoDock Vina
  • Receptor Preparation
  • Ligand Preparation
  • Generating AutoGrid4 Maps (Optional)
  • Docking with the AutoDock Vina Scoring Function
  • Docking with the AutoDock4 Scoring Function
  • Comparison of the Vina and AutoDock4 Force Fields
• Boltz-2
  • Introduction
  • Downloading the FASTA Sequence from the PDB Database
  • Creating a Boltz-2 Input File
  • Running the Calculation
  • Output Files
  • Visualizing the Predicted Structure
• Comparison of the Prediction with the Crystal Structure
  • Interpretation of the Results
  • Further Applications
• Gaussian
  • Structure of a Gaussian Input File
  • Running Gaussian Calculations
  • Example 1: Geometry Optimization of a Water Molecule
  • Example 2 - Frequency Calculation and Thermochemistry of Ethanol
  • Example 3: UV-Vis Spectrum Calculation of Caffeine Using TD-DFT
  • Example 4: NMR Chemical Shift Calculation for Methane
  • Example 5: Transition State Search for an SN2 Reaction
  • Example 6: Accounting for Solvent Effects Using the SMD Model
• GROMACS
  • Test System
  • Preparation of the Input Structure
  • Topology Generation
  • System Box Construction and Solvation
  • Adding Ions
  • Energy Minimization
  • NVT Equilibration
  • NPT Equilibration
  • Production Run
  • Analysis: Backbone RMSD Calculation
• MOPAC
  • Structure of a MOPAC Input File
  • Test System
  • Single-Point Energy Calculation
  • Geometry Optimization
  • Frequency Calculation
  • Solvent Effects - COSMO Model
  • Commonly Used MOPAC Keywords
• ORCA
  • Introduction
  • Structure of an ORCA Input File
  • Running ORCA
  • Example 1 - Geometry Optimization of a Water Molecule
  • Example 2 - Frequency Calculation and Thermochemistry of Ethanol
  • Example 3: UV-Vis Spectrum Calculation of Caffeine Using TDDFT
  • Example 4 - Calculation of NMR Chemical Shifts for Methane
  • Example 5 - Transition State Search for an SN2 Reaction
  • Example 6 - Including Solvent Effects in ORCA
  • Example 7 - High-Accuracy Energy Calculation Using DLPNO-CCSD(T)
  • Most Commonly Used ORCA Keywords
  • Parallel Execution and Memory Usage