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Topology Statement
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XPLOR Interface Manual
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Examples
Topology, Parameters and Molecular Structure
Subsections
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
Xplor-NIH 2023-11-10
