Topology, Parameters and Molecular Structure

• Topology Statement
  • Syntax
  • Example: Topology of a Leucine Amino Acid
• Parameter Statement
  • Syntax
  • Requirements
• Writing a Parameter File
  • Syntax
  • Example of Type-based Parameters
  • How the Type-based Parameter Retrieval Works
  • Examples of Atom-based Modifications of the Parameters
• Learning Atom-based Parameters
  • Requirements
  • Example: Learning Unknown Equilibrium Parameters from Coordinates
  • Example: Learning Atom-based Parameters from an Ensemble of Structures
• Reducing to Type-based Parameters
  • Syntax
  • Example: Reducing Parameters Learned Previously
• Topology and Parameter Files
  • CHARMM ``top_all22*" and ``par_all22*" All Hydrogen Force Field
  • CHARMM ``toph19.pro" and ``param19.pro" Files for Proteins (Explicit Polar Hydrogens)
  • CHARMM ``toph11.dna" and ``param11.dna" Files for Nucleic Acids (Explicit Polar Hydrogens)
  • Files ``topnah1e.dna" and ``parnah1e.dna" for Nucleic Acids (Explicit All Hydrogens)
  • AMBER/OPLS ``tophopls.pro", ``parhopls.pro" Files (Explicit Polar Hydrogens)
  • Files ``toph19.sol" and ``param19.sol" for Water (TIP3p Model)
  • Files ``toph3.cho" and ``param3.cho" for Carbohydrates
  • Files ``toph19.chromo" and ``param19.chromo" for Chromophores
  • Files ``parhcsdx.pro" and ``tophcsdx.pro" for Crystallographic Refinement (Polar Hydrogens)
  • Files ``parallhdg.pro" and ``topallhdg.pro" for NMR Structure Determination of Proteins (All Hydrogens)
    • Van der Waals radii
    • Convention for Hydrogen Names
  • Files ``parallhdg.dna" and ``topallhdg.dna" for NMR Structure Determination of Nucleic Acids (All Hydrogens)
• Generating the Molecular Structure
  • Syntax
  • Requirements
  • Example: A Polypeptide Chain
  • Example: A Polypeptide Chain with an Unknown Section
  • Example: Water Molecules
  • Example: Solvation of a Solute
• Patching the Molecular Structure
  • Syntax
  • Requirements
  • Example: Incorporation of Disulfide Bridges
  • Example: Modification of the Protonation Degree of Histidines
• Deleting Atoms
  • Syntax
  • Requirements
  • Example: Delete One Atom
• Duplicating the Molecular Structure
  • Syntax
  • Requirements
  • Example: Duplication of Side-Chain Atoms
• Structure Statement
  • Syntax
  • Requirements
  • Example: How to Read a Molecular Structure File
  • Example: Append Two Molecular Structure Files
• Writing a Molecular Structure File
  • Syntax
• Examples for Molecular Structure Generation
  • What to Do about Unknown Atoms
  • A Standard Protein Structure
  • How to Set Up Unusual Geometries
  • A Protein Structure with Water or Ligands
  • A Protein Structure with a Cofactor or Substrate
  • A Protein Structure with a Metal Cluster
  • A Nucleic Acid Structure
  • Virus Structures or Structures with Many Identical Units