Skip to main content
U.S. flag

An official website of the United States government

Here’s how you know

Official government website icon

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

icon-https

Secure .gov websites use HTTPS
A lock ( Lock Locked padlock icon )or https:// means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.

NIH: National Institute of Diabetes and Digestive and Kidney Diseases NIH: National Institute of Diabetes and Digestive and Kidney Diseases

  next up previous contents index  Xplor-NIH home Documentation

Next: Ab Initio SA Starting Up: Distance Geometry Previous: SA-Regularization of DG-Structures


Full-Structure Distance Geometry

This example input file shows how to produce a family of embedded coordinates using distance geometry that starts with regularized substructures. If metrization is desired, the appropriate lines should be uncommented. The names of the family of embedded coordinates will be “dg full embed 1.pdb" through “dg full embed 10.pdb". Although the “dg_full_embed.inp" protocol contains some regularization of the coordinates, further regularization is required by the “dgsa.inp" simulated annealing protocol.

Disulfide bonds and other covalent links should be treated in the same fashion as in the prior template generation. The removed covalent links are reintroduced as distance restraints.

dg_full_embed.inp



Xplor-NIH 2025-03-21
  • Privacy Policy
  • Freedom of Information Act
  • Accessibility
  • Disclaimers
  • Copyright
  • Vulnerability Disclosure Policy
  • U.S. Department of Health and Human Services
  • National Institutes of Health