Topology, Parameters and Molecular Structure
Subsections
- Topology Statement
- Parameter Statement
- 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
- 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)
- 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
- Duplicating the Molecular Structure
- Structure Statement
- Syntax
- Requirements
- Example: How to Read a Molecular Structure File
- Example: Append Two Molecular Structure Files
- Writing a Molecular Structure File
- 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
Xplor-NIH 2025-03-21