U.S. flag

An official website of the United States government
bit Xplor-NIH VMD-XPLOR
  next up previous contents index  Xplor-NIH home Documentation

Next: Topology and Parameter Files Up: Reducing to Type-based Parameters Previous: Syntax

Example: Reducing Parameters Learned Previously

Suppose one has learned atom-based parameters for a ligand with segment identifier LIGA from Cartesian coordinates. These atom-based parameters are reduced to type-based parameters and then written to a file: 
parameters reduce sele=(segid LIGA ) mode=average end end
write parameters output=newparameters.pro end
For each bonded pair of chemical types, an equilibrium geometry is obtained by averaging the atom-based parameters of all the bonds in the molecular structure that match this chemical type pair. For example, in a protein, this could imply averaging over all $C-C$ bonds in aromatic rings, or all $C-O$ carbonyl bonds. The same averaging is done for bond angles, dihedrals and impropers, equilibrium geometries, and energy constants. Dihedral and improper periodicities will correspond to their atom-based values. The new parameter file “newparameters.pro" can be read by X-PLOR in subsequent runs.
Xplor-NIH 2025-11-07